Full wwPDB X-ray Structure Validation Report...
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Full wwPDB X-ray Structure Validation Report i ○ Mar 14, 2018 – 01:10 pm GMT PDB ID : 4V7W Title : Structure of the Thermus thermophilus ribosome complexed with chloram- phenicol. Authors : Bulkley, D.P.; Innis, C.A.; Blaha, G.; Steitz, T.A. Deposited on : 2010-08-16 Resolution : 3.00 Å(reported) This is a Full wwPDB X-ray Structure Validation Report for a publicly released PDB entry. We welcome your comments at [email protected] A user guide is available at https://www.wwpdb.org/validation/2017/XrayValidationReportHelp with specific help available everywhere you see the i ○ symbol. The following versions of software and data (see references i ○) were used in the production of this report: MolProbity : 4.02b-467 Mogul : 1.7.3 (157068), CSD as539be (2018) Xtriage (Phenix) : 1.13 EDS : trunk31020 Percentile statistics : 20171227.v01 (using entries in the PDB archive December 27th 2017) Refmac : 5.8.0158 CCP4 : 7.0 (Gargrove) Ideal geometry (proteins) : Engh & Huber (2001) Ideal geometry (DNA, RNA) : Parkinson et al. (1996) Validation Pipeline (wwPDB-VP) : trunk31020
Transcript of Full wwPDB X-ray Structure Validation Report...
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Full wwPDB X-ray Structure Validation Report i
Mar 14, 2018 01:10 pm GMT
PDB ID : 4V7WTitle : Structure of the Thermus thermophilus ribosome complexed with chloram-
phenicol.Authors : Bulkley, D.P.; Innis, C.A.; Blaha, G.; Steitz, T.A.
Deposited on : 2010-08-16Resolution : 3.00 (reported)
This is a Full wwPDB X-ray Structure Validation Report for a publicly released PDB entry.
We welcome your comments at [email protected] user guide is available at
https://www.wwpdb.org/validation/2017/XrayValidationReportHelpwith specific help available everywhere you see the i symbol.
The following versions of software and data (see references i) were used in the production of this report:
MolProbity : 4.02b-467Mogul : 1.7.3 (157068), CSD as539be (2018)
Xtriage (Phenix) : 1.13EDS : trunk31020
Percentile statistics : 20171227.v01 (using entries in the PDB archive December 27th 2017)Refmac : 5.8.0158CCP4 : 7.0 (Gargrove)
Ideal geometry (proteins) : Engh & Huber (2001)Ideal geometry (DNA, RNA) : Parkinson et al. (1996)
Validation Pipeline (wwPDB-VP) : trunk31020
https://www.wwpdb.org/validation/2017/XrayValidationReportHelphttps://www.wwpdb.org/validation/2017/XrayValidationReportHelphttps://www.wwpdb.org/validation/2017/XrayValidationReportHelphttps://www.wwpdb.org/validation/2017/XrayValidationReportHelp#references
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Page 2 Full wwPDB X-ray Structure Validation Report 4V7W
1 Overall quality at a glance i
The following experimental techniques were used to determine the structure:X-RAY DIFFRACTION
The reported resolution of this entry is 3.00 .
Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown inthe following graphic. The table shows the number of entries on which the scores are based.
Metric Whole archive(#Entries)Similar resolution
(#Entries, resolution range())Rfree 111664 1851 (3.00-3.00)
Clashscore 122126 2167 (3.00-3.00)Ramachandran outliers 120053 2101 (3.00-3.00)
Sidechain outliers 120020 2104 (3.00-3.00)RSRZ outliers 108989 1751 (3.00-3.00)RNA backbone 2636 1017 (3.30-2.70)
The table below summarises the geometric issues observed across the polymeric chains and their fitto the electron density. The red, orange, yellow and green segments on the lower bar indicate thefraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria. Agrey segment represents the fraction of residues that are not modelled. The numeric value for eachfraction is indicated below the corresponding segment, with a dot representing fractions
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Page 3 Full wwPDB X-ray Structure Validation Report 4V7W
Continued from previous page...Mol Chain Length Quality of chain
3 AC 239
3 CC 239
4 AD 209
4 CD 209
5 AE 162
5 CE 162
6 AF 101
6 CF 101
7 AG 156
7 CG 156
8 AH 138
8 CH 138
9 AI 128
9 CI 128
10 AJ 105
10 CJ 105
11 AK 129
11 CK 129
12 AL 135
12 CL 135
13 AM 126
13 CM 126
14 AN 61
14 CN 61
15 AO 89Continued on next page...
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Page 4 Full wwPDB X-ray Structure Validation Report 4V7W
Continued from previous page...Mol Chain Length Quality of chain
15 CO 89
16 AP 88
16 CP 88
17 AQ 105
17 CQ 105
18 AR 88
18 CR 88
19 AS 93
19 CS 93
20 AT 106
20 CT 106
21 AU 27
21 CU 27
22 B0 85
22 D0 85
23 B1 98
23 D1 98
24 B2 72
24 D2 72
25 B3 60
25 D3 60
26 B4 71
26 D4 71
27 B5 60
27 D5 60Continued on next page...
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Page 5 Full wwPDB X-ray Structure Validation Report 4V7W
Continued from previous page...Mol Chain Length Quality of chain
28 B6 54
28 D6 54
29 B7 49
29 D7 49
30 B8 65
30 D8 65
31 BA 2787
31 DA 2787
32 BB 122
32 DB 122
33 BD 276
33 DD 276
34 BE 206
34 DE 206
35 BF 210
35 DF 210
36 BG 182
36 DG 182
37 BH 180
37 DH 180
38 BI 148
38 DI 148
39 BN 140
39 DN 140
40 BO 122Continued on next page...
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Continued from previous page...Mol Chain Length Quality of chain
40 DO 122
41 BP 150
41 DP 150
42 BQ 141
42 DQ 141
43 BR 118
43 DR 118
44 BS 112
44 DS 112
45 BT 146
45 DT 146
46 BU 118
46 DU 118
47 BV 101
47 DV 101
48 BW 113
48 DW 113
49 BX 96
49 DX 96
50 BY 110
50 DY 110
51 BZ 206
51 DZ 206
The following table lists non-polymeric compounds, carbohydrate monomers and non-standardresidues in protein, DNA, RNA chains that are outliers for geometric or electron-density-fit crite-ria:
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Mol Type Chain Res Chirality Geometry Clashes Electron density52 MG AA 1637 - - - X52 MG AA 1643 - - - X52 MG AA 1644 - - - X52 MG AA 1654 - - - X52 MG BA 3007 - - - X52 MG BA 3072 - - - X52 MG BA 3074 - - - X52 MG BA 3088 - - - X52 MG BA 3128 - - - X52 MG BA 3131 - - - X52 MG BA 3150 - - - X52 MG BA 3159 - - - X52 MG BA 3167 - - - X52 MG BA 3171 - - - X52 MG BA 3175 - - - X52 MG BA 3176 - - - X52 MG BA 3180 - - - X52 MG BA 3247 - - - X52 MG BA 3313 - - - X52 MG BA 3330 - - - X52 MG BA 3337 - - - X52 MG BA 3349 - - - X52 MG BA 3355 - - - X52 MG BA 3358 - - - X52 MG CA 1626 - - - X52 MG CA 1627 - - - X52 MG CA 1630 - - - X52 MG CA 1638 - - - X52 MG DA 3025 - - - X52 MG DA 3074 - - - X52 MG DA 3075 - - - X52 MG DA 3106 - - - X52 MG DA 3149 - - - X52 MG DA 3153 - - - X52 MG DA 3166 - - - X52 MG DA 3180 - - - X52 MG DA 3187 - - - X52 MG DA 3195 - - - X52 MG DA 3208 - - - X52 MG DA 3232 - - - X52 MG DA 3236 - - - X52 MG DA 3243 - - - X52 MG DA 3252 - - - X
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Continued from previous page...Mol Type Chain Res Chirality Geometry Clashes Electron density52 MG DA 3267 - - - X52 MG DA 3271 - - - X52 MG DA 3274 - - - X52 MG DA 3280 - - - X52 MG DA 3281 - - - X52 MG DA 3283 - - - X52 MG DA 3289 - - - X52 MG DA 3290 - - - X52 MG DA 3295 - - - X52 MG DA 3297 - - - X52 MG DA 3305 - - - X52 MG DA 3310 - - - X52 MG DA 3325 - - - X52 MG DA 3328 - - - X52 MG DU 201 - - - X53 ZN CD 301 - - X -
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2 Entry composition i
There are 55 unique types of molecules in this entry. The entry contains 277987 atoms, of which0 are hydrogens and 0 are deuteriums.
In the tables below, the ZeroOcc column contains the number of atoms modelled with zero occu-pancy, the AltConf column contains the number of residues with at least one atom in alternateconformation and the Trace column contains the number of residues modelled with at most 2atoms.
Molecule 1 is a RNA chain called 16S rRNA.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
1 AA 1504 Total C N O P32329 14390 5992 10444 1503 0 0 0
1 CA 1504 Total C N O P32329 14390 5992 10444 1503 0 0 0
Molecule 2 is a protein called 30S ribosomal protein S2.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
2 AB 235 Total C N O S1901 1213 342 341 5 0 0 1
2 CB 235 Total C N O S1901 1213 342 341 5 0 0 1
Molecule 3 is a protein called 30S ribosomal protein S3.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
3 AC 207 Total C N O S1613 1016 315 281 1 0 0 1
3 CC 207 Total C N O S1613 1016 315 281 1 0 0 1
Molecule 4 is a protein called 30S ribosomal protein S4.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
4 AD 208 Total C N O S1703 1066 339 291 7 0 0 0
4 CD 208 Total C N O S1703 1066 339 291 7 0 0 0
Molecule 5 is a protein called 30S ribosomal protein S5.
https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#entry_composition
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Mol Chain Residues Atoms ZeroOcc AltConf Trace
5 AE 151 Total C N O S1147 724 218 201 4 0 0 1
5 CE 151 Total C N O S1147 724 218 201 4 0 0 1
Molecule 6 is a protein called 30S ribosomal protein S6.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
6 AF 101 Total C N O S843 531 155 154 3 0 0 0
6 CF 101 Total C N O S843 531 155 154 3 0 0 0
Molecule 7 is a protein called 30S ribosomal protein S7.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
7 AG 155 Total C N O S1257 781 252 218 6 0 0 0
7 CG 155 Total C N O S1257 781 252 218 6 0 0 0
Molecule 8 is a protein called 30S ribosomal protein S8.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
8 AH 138 Total C N O S1116 705 215 193 3 0 0 0
8 CH 138 Total C N O S1116 705 215 193 3 0 0 0
Molecule 9 is a protein called 30S ribosomal protein S9.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
9 AI 127 Total C N O1011 639 198 174 0 0 0
9 CI 127 Total C N O1011 639 198 174 0 0 0
There are 2 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceAI 58 ARG HIS CONFLICT UNP P80374CI 58 ARG HIS CONFLICT UNP P80374
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Molecule 10 is a protein called 30S ribosomal protein S10.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
10 AJ 99 Total C N O S795 499 157 138 1 0 0 1
10 CJ 99 Total C N O S795 499 157 138 1 0 0 1
Molecule 11 is a protein called 30S ribosomal protein S11.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
11 AK 119 Total C N O S885 549 168 165 3 0 0 0
11 CK 119 Total C N O S885 549 168 165 3 0 0 0
Molecule 12 is a protein called 30S ribosomal protein S12.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
12 AL 125 Total C N O S971 611 196 163 1 0 0 1
12 CL 125 Total C N O S971 611 196 163 1 0 0 1
There are 6 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceAL 2 VAL - INSERTION UNP Q5SHN3AL 3 ALA - INSERTION UNP Q5SHN3AL 4 LEU - INSERTION UNP Q5SHN3CL 2 VAL - INSERTION UNP Q5SHN3CL 3 ALA - INSERTION UNP Q5SHN3CL 4 LEU - INSERTION UNP Q5SHN3
Molecule 13 is a protein called 30S ribosomal protein S13.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
13 AM 115 Total C N O S921 569 190 160 2 0 0 0
13 CM 115 Total C N O S921 569 190 160 2 0 0 0
Molecule 14 is a protein called 30S ribosomal protein S14.
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Mol Chain Residues Atoms ZeroOcc AltConf Trace
14 AN 60 Total C N O S492 312 104 72 4 0 0 0
14 CN 60 Total C N O S492 312 104 72 4 0 0 0
Molecule 15 is a protein called 30S ribosomal protein S15.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
15 AO 88 Total C N O S734 459 147 126 2 0 0 0
15 CO 88 Total C N O S734 459 147 126 2 0 0 0
Molecule 16 is a protein called 30S ribosomal protein S16.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
16 AP 84 Total C N O S701 443 140 117 1 0 0 1
16 CP 84 Total C N O S701 443 140 117 1 0 0 1
Molecule 17 is a protein called 30S ribosomal protein S17.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
17 AQ 100 Total C N O S824 528 152 142 2 0 0 1
17 CQ 100 Total C N O S824 528 152 142 2 0 0 1
Molecule 18 is a protein called 30S ribosomal protein S18.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
18 AR 70 Total C N O574 367 112 95 0 0 0
18 CR 70 Total C N O574 367 112 95 0 0 0
Molecule 19 is a protein called 30S ribosomal protein S19.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
19 AS 79 Total C N O S630 403 115 110 2 0 0 1
Continued on next page...
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Continued from previous page...Mol Chain Residues Atoms ZeroOcc AltConf Trace
19 CS 79 Total C N O S630 403 115 110 2 0 0 1
Molecule 20 is a protein called 30S ribosomal protein S20.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
20 AT 99 Total C N O S763 470 162 129 2 0 0 0
20 CT 99 Total C N O S763 470 162 129 2 0 0 0
Molecule 21 is a protein called 30S ribosomal protein Thx.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
21 AU 25 Total C N O209 128 51 30 0 0 1
21 CU 25 Total C N O209 128 51 30 0 0 1
Molecule 22 is a protein called 50S ribosomal protein L27.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
22 B0 85 Total C N O S650 401 137 111 1 0 0 0
22 D0 85 Total C N O S650 401 137 111 1 0 0 0
Molecule 23 is a protein called 50S ribosomal protein L28.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
23 B1 89 Total C N O693 435 140 118 0 0 1
23 D1 89 Total C N O693 435 140 118 0 0 1
Molecule 24 is a protein called 50S ribosomal protein L29.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
24 B2 51 Total C N O S421 263 85 72 1 0 0 1
24 D2 51 Total C N O S421 263 85 72 1 0 0 1
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Molecule 25 is a protein called 50S ribosomal protein L30.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
25 B3 60 Total C N O S468 298 91 78 1 0 0 1
25 D3 60 Total C N O S468 298 91 78 1 0 0 1
Molecule 26 is a protein called 50S ribosomal protein L31.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
26 B4 32 Total C N O157 93 32 32 0 0 0
26 D4 32 Total C N O157 93 32 32 0 0 0
Molecule 27 is a protein called 50S ribosomal protein L32.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
27 B5 59 Total C N O S459 288 90 76 5 0 0 0
27 D5 59 Total C N O S459 288 90 76 5 0 0 0
Molecule 28 is a protein called 50S ribosomal protein L33.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
28 B6 45 Total C N O S381 235 78 64 4 0 0 1
28 D6 45 Total C N O S381 235 78 64 4 0 0 1
Molecule 29 is a protein called 50S ribosomal protein L34.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
29 B7 49 Total C N O S419 257 105 55 2 0 0 1
29 D7 49 Total C N O S419 257 105 55 2 0 0 1
Molecule 30 is a protein called 50S ribosomal protein L35.
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Mol Chain Residues Atoms ZeroOcc AltConf Trace
30 B8 64 Total C N O S508 326 102 78 2 0 0 1
30 D8 64 Total C N O S508 326 102 78 2 0 0 1
Molecule 31 is a RNA chain called 23S ribosomal RNA.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
31 BA 2725 Total C N O P58698 26124 10986 18864 2724 0 0 0
31 DA 2725 Total C N O P58698 26124 10986 18864 2724 0 0 0
Molecule 32 is a RNA chain called 5S ribosomal RNA.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
32 BB 119 Total C N O P2551 1136 471 826 118 0 0 0
32 DB 119 Total C N O P2551 1136 471 826 118 0 0 0
Molecule 33 is a protein called 50S ribosomal protein L2.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
33 BD 272 Total C N O S2105 1329 417 356 3 0 0 1
33 DD 272 Total C N O S2105 1329 417 356 3 0 0 1
Molecule 34 is a protein called 50S ribosomal protein L3.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
34 BE 205 Total C N O S1564 988 300 270 6 0 0 1
34 DE 205 Total C N O S1564 988 300 270 6 0 0 1
Molecule 35 is a protein called 50S ribosomal protein L4.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
35 BF 208 Total C N O S1624 1035 304 282 3 0 0 1
Continued on next page...
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Continued from previous page...Mol Chain Residues Atoms ZeroOcc AltConf Trace
35 DF 208 Total C N O S1624 1035 304 282 3 0 0 1
Molecule 36 is a protein called 50S ribosomal protein L5.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
36 BG 181 Total C N O S1474 942 268 260 4 0 0 0
36 DG 181 Total C N O S1474 942 268 260 4 0 0 0
Molecule 37 is a protein called 50S ribosomal protein L6.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
37 BH 160 Total C N O S1223 773 229 220 1 0 0 1
37 DH 160 Total C N O S1223 773 229 220 1 0 0 1
Molecule 38 is a protein called 50S ribosomal protein L9.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
38 BI 146 Total C N O S1132 723 201 207 1 0 0 1
38 DI 146 Total C N O S1132 723 201 207 1 0 0 1
Molecule 39 is a protein called 50S ribosomal protein L13.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
39 BN 139 Total C N O S1105 712 207 182 4 0 0 1
39 DN 139 Total C N O S1105 712 207 182 4 0 0 1
Molecule 40 is a protein called 50S ribosomal protein L14.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
40 BO 122 Total C N O S933 588 171 170 4 0 0 0
40 DO 122 Total C N O S933 588 171 170 4 0 0 0
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Molecule 41 is a protein called 50S ribosomal protein L15.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
41 BP 146 Total C N O S1114 692 227 193 2 0 0 0
41 DP 146 Total C N O S1114 692 227 193 2 0 0 0
Molecule 42 is a protein called 50S ribosomal protein L16.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
42 BQ 136 Total C N O S1080 688 204 183 5 0 0 0
42 DQ 136 Total C N O S1080 688 204 183 5 0 0 0
Molecule 43 is a protein called 50S ribosomal protein L17.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
43 BR 117 Total C N O960 599 202 159 0 0 0
43 DR 117 Total C N O960 599 202 159 0 0 0
Molecule 44 is a protein called 50S ribosomal protein L18.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
44 BS 99 Total C N O771 486 155 130 0 0 1
44 DS 99 Total C N O771 486 155 130 0 0 1
Molecule 45 is a protein called 50S ribosomal protein L19.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
45 BT 132 Total C N O S1100 686 227 186 1 0 0 0
45 DT 132 Total C N O S1100 686 227 186 1 0 0 0
Molecule 46 is a protein called 50S ribosomal protein L20.
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Mol Chain Residues Atoms ZeroOcc AltConf Trace
46 BU 117 Total C N O S958 604 202 151 1 0 0 0
46 DU 117 Total C N O S958 604 202 151 1 0 0 0
Molecule 47 is a protein called 50S ribosomal protein L21.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
47 BV 101 Total C N O S779 501 142 135 1 0 0 0
47 DV 101 Total C N O S779 501 142 135 1 0 0 0
Molecule 48 is a protein called 50S ribosomal protein L22.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
48 BW 113 Total C N O S896 563 176 155 2 0 0 0
48 DW 113 Total C N O S896 563 176 155 2 0 0 0
Molecule 49 is a protein called 50S ribosomal protein L23.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
49 BX 93 Total C N O726 471 132 123 0 0 1
49 DX 93 Total C N O726 471 132 123 0 0 1
Molecule 50 is a protein called 50S ribosomal protein L24.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
50 BY 101 Total C N O S776 500 149 123 4 0 0 1
50 DY 101 Total C N O S776 500 149 123 4 0 0 1
Molecule 51 is a protein called 50S ribosomal protein L25.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
51 BZ 177 Total C N O S1404 897 253 252 2 0 0 1
Continued on next page...
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Continued from previous page...Mol Chain Residues Atoms ZeroOcc AltConf Trace
51 DZ 177 Total C N O S1404 897 253 252 2 0 0 1
Molecule 52 is MAGNESIUM ION (three-letter code: MG) (formula: Mg).
Mol Chain Residues Atoms ZeroOcc AltConf
52 BA 368 Total Mg368 368 0 0
52 CA 53 Total Mg53 53 0 0
52 DQ 1 Total Mg1 1 0 0
52 DF 1 Total Mg1 1 0 0
52 BE 1 Total Mg1 1 0 0
52 DU 1 Total Mg1 1 0 0
52 B1 1 Total Mg1 1 0 0
52 BP 2 Total Mg2 2 0 0
52 DR 1 Total Mg1 1 0 0
52 B5 2 Total Mg2 2 0 0
52 BB 7 Total Mg7 7 0 0
52 BF 1 Total Mg1 1 0 0
52 BX 1 Total Mg1 1 0 0
52 AA 56 Total Mg56 56 0 0
52 BQ 2 Total Mg2 2 0 0
52 BU 1 Total Mg1 1 0 0
52 DD 1 Total Mg1 1 0 0
52 BR 2 Total Mg2 2 0 0
Continued on next page...
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Continued from previous page...Mol Chain Residues Atoms ZeroOcc AltConf
52 DA 332 Total Mg332 332 0 0
52 DE 1 Total Mg1 1 0 0
52 D1 1 Total Mg1 1 0 0
52 DX 1 Total Mg1 1 0 0
52 DP 1 Total Mg1 1 0 0
52 D5 2 Total Mg2 2 0 0
52 BD 1 Total Mg1 1 0 0
52 DB 4 Total Mg4 4 0 0
Molecule 53 is ZINC ION (three-letter code: ZN) (formula: Zn).
Mol Chain Residues Atoms ZeroOcc AltConf
53 CN 1 Total Zn1 1 0 0
53 AD 1 Total Zn1 1 0 0
53 CD 1 Total Zn1 1 0 0
53 AN 1 Total Zn1 1 0 0
Molecule 54 is POTASSIUM ION (three-letter code: K) (formula: K).
Mol Chain Residues Atoms ZeroOcc AltConf
54 BA 1 Total K1 1 0 0
54 DA 1 Total K1 1 0 0
Molecule 55 is CHLORAMPHENICOL (three-letter code: CLM) (formula: C11H12Cl2N2O5).
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Mol Chain Residues Atoms ZeroOcc AltConf
55 BA 1 Total C Cl N O20 11 2 2 5 0 0
55 DA 1 Total C Cl N O20 11 2 2 5 0 0
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3 Residue-property plots i
These plots are drawn for all protein, RNA and DNA chains in the entry. The first graphic fora chain summarises the proportions of the various outlier classes displayed in the second graphic.The second graphic shows the sequence view annotated by issues in geometryand electron density.Residues are color-coded according to the number of geometric quality criteria for which theycontain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. A red dotabove a residue indicates a poor fit to the electron density (RSRZ > 2). Stretches of 2 or moreconsecutive residues without any outlier are shown as a green connector. Residues present in thesample, but not in the model, are shown in grey.
Molecule 1: 16S rRNA
Chain AA:
U U U G U U5 G6 G7 A8 G9 A10
G11
U12
U13
U14
G15
A16
U17
C18
C19
U20
G21
G22
C23
U24
C25
A26
G27
G28
G29
U30
G31
A32
A33
C34
G35
C36
U37
G38
G39
C40
G41
G42
C43
G44
C47
C48
U49
A50
A51
G52
A53
C54
A55
U56
G57
C58
A59
A60
G61
U62
C63
G64
U65
G66
C67
G68
G69
G70
C71
C72
G73
C76
G77
G78
G79
G80
U81
U82
U83
U84
A88
C89
U90
C91
C92
G93
U96
G97
G98
U99
C100
A101
G102
C103
G104
G105
C106
G107
G108
A109
C110
G113
U114
G115
A116
G117
U118
A119
A120
C121
G122
C123
G124
U125
G126
A130
C131
C132
U133
A134
C135
C136
C137
G138
G139
G142
A143
G144
G145
G146
G147
G148
A149
C150
A151
A152
C155
G156
G159
A160
A161
A162
C163
U164
C165
G166
G167
G168
C169
U170
A171
A172
U173
C176
C177
C178
A179
U180
G181
U182
G183
G184
A185
C186
C187
C188
G189
C189
AC1
89B
C189
CC1
89D
U189
E
U189
FG1
89G
G189
HG1
89I
G189
JU1
89K
G189
LU1
90G1
91
U192
C193
C194
A195
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https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#residue_plots
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Page 23 Full wwPDB X-ray Structure Validation Report 4V7W
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531
U C A C C U C C U U U C U
Molecule 1: 16S rRNA
Chain CA:
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Page 24 Full wwPDB X-ray Structure Validation Report 4V7W
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C590
U591
G592
G593
G594
U598
C599
C600
C601
A602
U603
G604
U605
G606
A607
A608
C612
C613
A614
C615
G616
G617
C618
U619
C620
A621
A622
C623
C624
G625
U626
G627
G628
G629
G630
G631
A632
G633
C634
G635
U636
G639
A640
U641
A642
C645
U646
C647
G650
C651
U652
A653
G654
A655
C656
G657
G658
U659
G660
G661
G662
A663
G664
A665
G666
G667
G668
U669
G670
G671
U672
G673
G674
A675
A676
U677
U678
C679
C680
C681
G682
G683
A684
G685
U686
A687
G688
C689
G690
G691
U692
G693
A694
A695
A696
U697
C701
A702
G703
A704
U705
A706
C707
C708
G709
G710
G713
G714
A715
A716
C717
G718
C719
C720
G721
A722
U723
G724
G725
C726
G727
A728
A729
G730
G731
C732
A733
G734
C735
C736
A737
C738
C739
U740
G741
G742
U743
C744
C745
A746
C747
C748
C749
G750
A753
C754
G755
C756
U757
G758
A759
G760
G763
C764
G765
A766
A767
A768
G769
C770
G771
G774
G775
G776
A777
G778
C779
A780
A781
A782
C783
C784
G785
G786
A787
U788
U789
A790
G791
A792
U793
A794
C797
G803
U804
C805
C806
A807
C808
G809
C810
C811
A814
A815
A816
C817
G818
A819
U820
G821
C822
G823
C824
G825
C826
U827
A828
G829
G830
U831
C832
U833
C834
U835
G836
U839
C840
U841
C848
G851
G852
G853
G854
G855
C856
C857
G858
A859
A860
G861
C862
U863
A864
A865
C868
G869
U870
U871
A872
A873
G874
C875
G876
C877
G878
C879
C880
G881
C882
C883
U884
G885
A889
A892
C893
G894
G895
C896
C897
G898
C899
A900
A901
G902
G903
C904
A913
A914
A915
G916
G917
A918
A919
U920
U921
G922
A923
C924
G925
G926
G927
G928
G929
C930
C931
C932
G933
C934
A935
C936
A937
A938
G939
C940
G941
G942
U943
G944
G945
A946
G947
C948
A949
U950
G951
U952
G953
G954
U955
U956
U957
A958
A959
U960
U961
C962
G963
A964
A965
G966
C967
A968
A969
C970
G971
C972
G973
A974
A975
G976
A977
A978
C979
C980
U981
U982
A983
C984
C985
A986
G987
U991
U992
G993
A994
C995
A996
U997
G998
C999
U100
0
A100
1
G100
1A
G100
2
G100
3
A100
4
A100
5
C100
6
C100
7
C100
8
G100
9
G101
0G1
011
U101
2G1
013
A101
4A1
015
A101
6G1
017
C101
8
C101
9
U102
0
G102
1
G102
2
G102
3
G102
4
U102
5
G102
6
C102
7
C102
8
C102
9
C103
0
G103
0A
C103
0B
G103
0C
A103
0D
G103
1
G103
2
G103
3
G103
4
A103
5
-
Page 25 Full wwPDB X-ray Structure Validation Report 4V7W
G103
6
C103
7
C103
8
C103
9
U104
0
A104
1
G104
2
C104
3
A104
4C1
045
A104
6G1
047
G104
8U1
049
G105
0
C105
1U1
052
G105
3C1
054
A105
5U1
056
G105
7
G105
8C1
059
C106
0
C106
3G1
064
U106
5
C106
6
A106
7G1
068
C106
9
U107
0C1
071
G107
2U1
073
G107
4C1
075
C107
6G1
077
U107
8G1
079
A108
0G1
081
G108
2U1
083
G108
4U1
085
U108
6G1
087
G108
8G1
089
U109
0U1
091
A109
2
A109
3
G109
4U1
095
C109
6
C109
7
C109
8
A110
1A1
102
C110
3G1
104
A110
5G1
106
C110
7G1
108
C110
9
C111
2C1
113
C111
4C1
115
C111
6G1
117
C111
8C1
119
G112
0
U112
1U1
122
A112
3G1
124
U112
5U1
126
G112
7
C112
8
C112
9
A113
0
G113
1
C113
2
G113
3G1
134
U113
5U1
136
C113
7
G113
8G1
139
C114
0
C114
1
G114
2
G114
3G1
144
C114
5A1
146
C114
7U1
148
C114
9
U115
0
A115
1A1
152
C115
3G1
154
G115
5G1
156
A115
7
C115
8
U115
9G1
160
C116
1C1
162
C116
3
G116
4
C116
5
G116
6A1
168
A116
9A1
170
G117
1C1
172
G117
3G1
174
A117
9A1
180
G118
1G1
182
A118
3
G118
4
G118
5
G118
6
G118
7
A118
8C1
189
G119
0A1
191
C119
2G1
193
U119
4C1
195
U119
6G1
197
G119
8U1
199
C120
0A1
201
G120
2
C120
3A1
204
U120
5
G120
6G1
207
C120
8C1
209
C121
0U1
211
U121
2
A121
3C1
214
G121
5G1
216
C121
7C1
218
U121
9
G122
0G1
221
G122
2
C122
3
G122
4
A122
5
C122
6
A122
7
C122
8A1
229
C123
0G1
231
U123
2
G123
3
C123
4
U123
5
A123
6
C123
7A1
238
A123
9
U124
0
G124
1
C124
2
C124
3
C124
4
A124
5
C124
6U1
247
A124
8C1
249
A125
0A1
251
A125
2
G125
3C1
254
G125
5
A125
6U1
257
G125
8
C125
9C1
260
A126
1
C126
2
C126
3C1
264
G126
5
A126
9
C127
0G1
271
G127
2G1
273
G127
4A1
275
G127
6
C127
7
U127
8
A127
9A1
280
U128
1C1
282
G128
3
C128
4
A128
5
A128
6
A128
7
A128
8A1
289
G129
0G1
291
U129
2G1
293
G129
4
G129
5
C129
6
C129
7C1
298
A129
9G1
300
U130
1U1
302
C130
3
G130
4G1
305
A130
6
U130
7U1
308
G130
9G1
310
G131
1
G131
2
U131
3
C131
4
U131
5G1
316
C131
7A1
318
A131
9C1
320
C132
1
C132
2G1
323
A132
4C1
325
C132
6
C132
7
C132
8A1
329
U133
0G1
331
A133
2A1
333
G133
4C1
335
C133
6
G133
7G1
338
A133
9
C134
2G1
343
C134
4U1
345
A134
6G1
347
U134
8A1
349
A135
0U1
351
C135
2
G135
3
C135
4G1
355
G135
6A1
357
U135
8
G136
1C1
362
C136
3A1
363A
U136
4G1
365
C136
6C1
367
G136
8C1
369
G137
0
G137
1U1
372
G137
3A1
374
C137
8G1
379
U138
0U1
381
C138
2
G138
5
G138
6G1
387
C138
8C1
389
U139
0U1
391
G139
2
U139
3
C139
7A1
398
C139
9C1
400
G140
1C1
402
C140
3C1
404
G140
5U1
406
C140
7
G141
0C1
411
C141
2A1
413
U141
4G1
415
G141
6G1
417
A141
8G1
419
G142
2G1
423
C142
4U1
425
C142
6U1
427
A142
8C1
429
C143
0C1
431
G143
2A1
433
A143
4G1
435
U143
6
G144
1G1
442
G144
2A
A144
2BG1
443
U144
6A1
447
C145
2G1
456
A146
0G1
461
G146
4C1
465
C146
6G1
467
A146
8G1
469
G147
0
C147
7C1
478
C147
9G1
480
U148
1G1
482
A148
3C1
484
U148
5G1
486
G148
7
C149
0
G149
1A1
492
A149
3G1
494
U149
5C1
496
G149
7U1
498
A149
9A1
500
C150
1A1
502
A150
3
G150
4G1
505
U150
6A1
507
G150
8C1
509
U151
0G1
511
U151
2A1
513
C151
4C1
515
G151
6G1
517
A151
8A1
519
G152
0G1
521
U152
2
G152
5G1
526
C152
7U1
528
G152
9G1
530
A153
1
U C A C C U C C U U U C U
Molecule 2: 30S ribosomal protein S2
Chain AB:
MET
PRO
VAL
GLU
ILE
THR
V7
K8 E9 L10
L11
E12
A13
G14
V15
H16
F17
G18
H19
E20
R21
K22
R23
W24
N25
P26
K27
F28
A29
R30
Y31
I32
E35
R36
N37
G38
I39
H40
I41
I42
D43
L44
T47
M48
L51
E52
R53
T54
F55
R56
F57
I58
E59
D60
L61
A62
M63
R64
T67
I68
L69
F70
V71
K74
K75
Q76
A77
Q78
D79
I80
V81
E84
R87
A88
G89
M90
P91
Y92
Q95
R96
W97
L98
G99
G100
M101
L102
T103
N104
F105
K106
T107
I108
R111
V112
H113
R114
L115
E116
E117
L118
E119
A120
L121
S124
P125
E126
I127
E128
E129
R130
P131
K132
K133
E134
Q135
V136
R137
L138
K139
H140
E141
L142
E143
R144
L145
Q146
K147
Y148
L149
S150
G151
F152
R153
L154
L155
K156
R157
L158
P159
I162
F163
V164
V165
D166
P167
T168
K169
E170
A171
I172
A173
V174
R175
E176
A177
R178
K179
L180
F181
I185
A186
L187
A188
D189
T190
D191
S192
D193
P194
D195
L196
V197
D198
Y199
I200
I201
P202
G203
N204
D205
D206
A207
I208
R209
S210
I211
Q212
L213
I214
L215
S216
R217
A218
V219
D220
L221
I222
I223
Q224
A225
G228
V229
V230
E231
P232
S233
P234
L238
V239
Q240
E241
ALA
GLU
ALA
THR
GLU
THR
PRO
GLU
GLY
GLU
SER
GLU
VAL
GLU
ALA
Molecule 2: 30S ribosomal protein S2
Chain CB:
-
Page 26 Full wwPDB X-ray Structure Validation Report 4V7W
MET
PRO
VAL
GLU
ILE
THR
V7
K8 E9 L10
L11
E12
A13
G14
V15
H16
F17
G18
H19
E20
R21
K22
R23
W24
N25
P26
K27
F28
A29
R30
Y31
I32
Y33
A34
E35
R36
N37
G38
I39
H40
I41
I42
D43
L44
T47
L51
E52
R53
T54
F55
I58
E59
D60
L61
A62
M63
R64
T67
I68
L69
F70
V71
K74
K75
Q76
A77
Q78
D79
I80
V81
R82
M83
E84
R87
A88
G89
M90
P91
Y92
R96
W97
L98
G99
G100
M101
L102
T103
N104
F105
K106
T107
I108
S109
Q110
R111
V112
H113
R114
L115
E116
E117
L118
E119
A120
L121
S124
P125
E126
I127
E128
E129
R130
P131
K132
K133
E134
Q135
V136
R137
L138
K139
H140
E141
L142
E143
R144
L145
Q146
L149
S150
G151
F152
R153
L154
L155
K156
R157
L158
P159
I162
F163
V164
V165
D166
P167
T168
K169
E170
A171
I172
A173
V174
R175
E176
A177
R178
K179
L180
F181
I185
A186
L187
A188
D189
T190
D191
S192
D193
P194
D195
L196
V197
D198
Y199
I200
I201
P202
G203
N204
D205
D206
A207
I208
R209
S210
I211
Q212
L213
I214
L215
S216
R217
A218
V219
D220
L221
I222
I223
Q224
A225
G228
V229
V230
E231
P232
S233
P234
S235
Y236
A237
L238
V239
Q240
E241
ALA
GLU
ALA
THR
GLU
THR
PRO
GLU
GLY
GLU
SER
GLU
VAL
GLU
ALA
Molecule 3: 30S ribosomal protein S3
Chain AC:
MET
G2
N3
K4 I5 H6 P7 R11
L12
G13
I14
T15
R16
D17
W18
E19
S20
Y23
A24
K27
Q28
Y29
L32
L33
L34
E35
D36
Q37
R38
I39
R40
G41
L42
L43
E46
L47
A50
G51
L52
A53
R54
V55
D56
I57
E58
R59
A60
A61
D62
N63
V64
A65
V66
T67
V68
H69
V70
A71
K72
P73
V76
I77
G78
R79
E82
R83
V86
L87
R88
E89
E90
L91
A92
K93
L94
T95
V99
A100
L101
N102
V103
Q104
E105
V106
Q107
N108
P109
N110
L111
S112
A113
P114
L115
V116
A117
Q118
R119
V120
E125
R126
R127
V130
R131
R132
A133
I134
K135
Q136
A137
V138
Q139
R140
V141
M142
E143
S144
G145
A146
K147
G148
A149
K150
V151
I152
V153
S154
G155
R156
I157
G158
G159
A160
T165
E166
W167
A168
G171
R172
V173
P174
L175
L178
R179
A180
N181
I182
D183
Y184
G185
F186
A187
L188
A189
R190
T191
T192
Y193
G194
V195
L196
G197
V198
K199
A200
Y201
I202
F203
L204
V207
I208
GLY
GLY
GLN
LYS
PRO
LYS
ALA
ARG
PRO
GLU
LEU
PRO
LYS
ALA
GLU
GLU
ARG
PRO
ARG
ARG
ARG
ARG
PRO
ALA
VAL
ARG
VAL
LYS
LYS
GLU
GLU
Molecule 3: 30S ribosomal protein S3
Chain CC:
MET
G2
N3
K4 I5 H6 P7 R11
L12
G13
I14
T15
R16
D17
W18
E19
S20
Y23
A24
K27
Q28
Y29
L32
L33
L34
E35
D36
Q37
R38
I39
R40
G41
L42
L43
E44
K45
E46
L47
A50
G51
L52
A53
R54
V55
D56
I57
E58
R59
A60
A61
D62
N63
V64
A65
V66
T67
V68
H69
V70
A71
K72
P73
G74
V75
V76
I77
G78
R79
G80
G81
E82
R83
V86
L87
R88
E89
E90
L91
A92
K93
L94
T95
N98
V99
A100
L101
N102
V103
Q104
E105
V106
Q107
N108
P109
N110
L111
S112
A113
P114
L115
V116
A117
Q118
R119
V120
A121
E122
Q123
I124
E125
R126
R127
V130
R131
R132
A133
I134
K135
Q136
A137
V138
Q139
R140
V141
M142
G145
A146
K147
G148
A149
K150
V151
I152
V153
S154
G155
R156
I157
G158
G159
A160
T165
E166
W167
A168
G171
R172
V173
P174
L175
L178
R179
A180
N181
I182
D183
Y184
G185
F186
A187
L188
A189
R190
T191
T192
Y193
G194
V195
L196
A200
Y201
I202
F203
E206
V207
I208
GLY
GLY
GLN
LYS
PRO
LYS
ALA
ARG
PRO
GLU
LEU
PRO
LYS
ALA
GLU
GLU
ARG
PRO
ARG
ARG
ARG
ARG
PRO
ALA
VAL
ARG
VAL
LYS
LYS
GLU
GLU
-
Page 27 Full wwPDB X-ray Structure Validation Report 4V7W
Molecule 4: 30S ribosomal protein S4
Chain AD:
MET
G2 R3
Y4 I5 G6 P7 V8 C9 R10
L11
C12
R13
R14
E15
G16
V17
K18
L19
Y20
L21
K22
G23
E24
R25
C26
Y27
S28
P29
K30
C31
A32
M33
E34
R35
R36
P37
Y38
P39
P40
G41
Q42
H43
G44
Q45
K46
R47
A48
R49
V56
R57
L58
R59
E60
K61
Q62
K63
L64
R65
E72
R73
Q74
F75
R76
N77
L78
F79
E80
E81
V88
T89
G90
S91
V92
F93
L94
G95
L96
L97
E98
S99
R100
L101
D102
N103
Y106
R107
L108
G109
F110
A111
V112
S113
R114
R115
Q116
A117
R118
Q119
L120
V121
R122
H123
G124
H125
I126
T127
V128
N129
G130
R131
R132
V133
D134
L135
P136
S137
Y138
R139
V140
R141
P142
G143
D144
E145
I146
A147
V148
A149
E150
K151
S152
R153
N154
L155
E156
L157
I158
R159
Q160
N161
L162
E163
A164
M165
K166
V170
G171
P172
W173
L174
S175
G180
M181
K182
G183
K184
R187
L188
P189
D190
R191
L194
A195
L196
P197
E200
Q201
L202
V203
I204
E205
F206
Y207
S208
R209
Molecule 4: 30S ribosomal protein S4
Chain CD:
MET
G2 R3
Y4 I5 G6 P7
V8 C9 R10
L11
C12
R13
R14
E15
G16
V17
K18
L19
Y20
L21
K22
G23
E24
R25
C26
Y27
S28
P29
K30
C31
A32
M33
E34
R35
R36
P37
Y38
P39
P40
G41
Q42
H43
G44
Q45
K46
R47
A48
R49
V56
R57
L58
R59
E60
K61
Q62
K63
L64
R65
E72
R73
Q74
F75
R76
N77
L78
F79
E80
E81
V88
S91
V92
F93
L94
G95
L96
L97
E98
S99
R100
V105
Y106
R107
L108
G109
F110
A111
V112
Q116
A117
R118
Q119
L120
V121
R122
H123
G124
H125
I126
T127
V128
N129
G130
R131
R132
V133
D134
L135
P136
S137
Y138
R139
V140
R141
P142
G143
D144
E145
I146
A147
V148
A149
E150
K151
S152
R153
N154
L155
E156
L157
I158
R159
Q160
N161
L162
E163
A164
M165
K166
V170
G171
P172
W173
L174
S175
G180
M181
K182
G183
K184
R187
L188
P189
D190
R191
L194
A195
L196
P197
E200
Q201
L202
V203
I204
E205
F206
Y207
S208
R209
Molecule 5: 30S ribosomal protein S5
Chain AE:
MET
PRO
GLU
THR
D5 F6 E7 I11
L12
I13
R14
R15
R18
M19
Q20
A21
R25
F26
R27
F28
G29
A30
L31
V32
V33
V34
G35
D36
V41
G42
L43
G44
F45
G46
K47
E50
V51
P52
V55
Q56
K57
A58
Y61
M66
V67
E68
V69
P70
L71
Q72
T75
I76
P77
H78
E79
I80
E81
V82
G85
A86
S87
K88
I89
V90
L91
K92
P96
G97
T98
G99
V100
I101
A102
P106
R107
A108
I109
L110
E111
L112
A113
G114
V115
T116
D117
I118
L119
T120
K121
E122
S125
R126
N127
P128
I129
A132
T135
M136
E137
A138
L139
R140
Q141
L142
R143
T144
K145
A146
D147
V148
E149
R152
K153
G154
E155
ALA
HIS
ALA
GLN
ALA
GLN
GLY
Molecule 5: 30S ribosomal protein S5
Chain CE:
MET
PRO
GLU
THR
D5 F6
E7 I11
L12
I13
R14
R15
R18
M19
Q20
A21
R25
F26
R27
F28
G29
A30
L31
V32
V33
V34
G35
D36
R40
V41
G42
L43
G44
F45
G46
K47
E50
V51
P52
V55
Q56
K57
A58
Y61
M66
V67
E68
V69
P70
L71
Q72
-
Page 28 Full wwPDB X-ray Structure Validation Report 4V7W
T75
I76
P77
H78
E79
I80
E81
V82
G85
A86
S87
K88
I89
V90
L91
P96
G97
T98
G99
V100
I101
A102
P106
R107
A108
I109
L110
E111
L112
A113
G114
V115
T116
D117
I118
L119
T120
K121
E122
L123
G124
S125
R126
N127
P128
I129
N130
I131
A132
Y133
A134
T135
M136
E137
A138
L139
R140
Q141
L142
R143
T144
K145
A146
D147
V148
E149
R150
L151
R152
K153
G154
E155
ALA
HIS
ALA
GLN
ALA
GLN
GLY
Molecule 6: 30S ribosomal protein S6
Chain AF:
M1 R2 R3
Y4
E5 V6 N7 I8 V9 L10
N11
L14
D15
Q16
S17
Q18
L19
A20
L21
E22
K23
E24
I25
I26
Q27
R28
A29
L30
Y33
G34
A35
R36
V37
E38
K39
V40
E41
E42
L43
G44
L45
R46
Y50
P51
I52
A53
K54
D55
Y59
F60
L61
W62
Y63
Q64
V65
E66
M67
P68
E69
D70
R71
V72
N73
D74
L75
A76
R77
E78
L79
R80
I81
R82
D83
N84
V85
R86
R87
V88
M89
V90
V91
K92
S93
Q94
E95
P96
F97
L98
A99
N100
A101
Molecule 6: 30S ribosomal protein S6
Chain CF:
M1 R2 R3 Y4 E5 V6 N7 I8 V9 L10
N11
P12
N13
L14
D15
Q16
S17
Q18
L19
A20
L21
E22
K23
E24
I25
I26
Q27
R28
A29
L30
G34
A35
R36
V37
E38
K39
V40
E41
E42
L43
G44
L45
R46
Y50
P51
I52
A53
K54
D55
G58
Y59
F60
L61
W62
Y63
Q64
V65
E66
M67
P68
E69
D70
R71
V72
N73
D74
L75
A76
R77
E78
L79
R80
I81
R82
D83
N84
V85
R86
R87
V88
M89
V90
V91
K92
S93
Q94
E95
P96
F97
L98
A99
N100
A101
Molecule 7: 30S ribosomal protein S7
Chain AG:
MET
A2 R3
R4 R5
R6 A7 Q11
L12
Q13
P14
D15
L16
V17
Y18
G19
D20
V21
L22
V23
T24
A25
F26
I27
N28
K29
I30
M31
R32
D33
G34
K35
K36
N37
L38
A39
A40
R41
I42
F43
Y44
D45
A46
C47
K48
I49
I50
Q51
E52
L59
K60
V61
F62
N68
V69
K70
P71
R72
M73
E74
V75
R76
S77
R78
R79
V80
G81
G82
A83
N84
Y85
Q86
V87
P88
M89
E90
V91
S92
P93
R94
R95
Q96
Q97
S98
L99
A100
L101
R102
W103
L104
V105
Q106
A107
R111
P112
E113
R114
R115
A116
A117
V118
R119
I120
A121
H122
E123
L124
G133
A134
V135
K136
K137
K138
E139
D140
R143
M144
A145
E146
A147
N148
R149
A150
Y151
A152
H153
Y154
R155
W156
Molecule 7: 30S ribosomal protein S7
Chain CG:
MET
A2
R3
R4
R5
R6
A7 E8
L12
Q13
P14
D15
L16
V17
Y18
G19
L22
V23
T24
A25
F26
I27
N28
K29
I30
M31
R32
D33
G34
K35
K36
N37
L38
A39
A40
R41
I42
F43
Y44
D45
A46
C47
K48
I49
I50
L59
K60
V61
F62
N68
V69
K70
M73
E74
V75
R76
S77
R78
R79
V80
G81
G82
A83
N84
Y85
Q86
V87
P88
M89
E90
V91
R94
R95
Q96
Q97
S98
L99
A100
L101
R102
W103
L104
V105
Q106
A107
Q110
R111
P112
E113
R114
R115
A116
A117
V118
R119
H122
E123
L124
G130
K131
G132
G133
A134
K138
E139
D140
R143
M144
A145
-
Page 29 Full wwPDB X-ray Structure Validation Report 4V7W
E146
A147
N148
R149
A150
Y151
A152
H153
Y154
R155
W156
Molecule 8: 30S ribosomal protein S8
Chain AH:
M1 L2 P5 I6 A7 D8 M9 L10
T11
R12
I13
R14
N15
A16
T17
Y20
K21
E22
S23
T24
D25
V26
P27
A28
S29
R30
F31
K32
E33
E34
I35
L36
R37
I38
L39
A40
R41
E42
G43
F44
I45
V51
D52
V53
D54
P57
Y58
L59
R60
L63
K64
Y65
R68
P72
E77
Q78
V79
I80
I83
R84
R85
I86
S87
K88
P89
G90
R91
R92
V93
Y94
V95
G96
V97
I100
P101
R102
V103
A110
I111
L112
S113
T114
S115
K116
L119
T120
E123
L127
G128
V129
E132
L133
I134
C135
W138
Molecule 8: 30S ribosomal protein S8
Chain CH:
M1 L2 T3 D4 P5 I6 A7 D8 M9 L10
T11
R12
I13
R14
N15
A16
T17
Y20
K21
E22
S23
T24
D25
V26
P27
A28
S29
R30
F31
K32
E33
E34
I35
L36
R37
I38
L39
A40
R41
E42
G43
F44
I45
V51
D52
V53
D54
P57
Y58
L59
R60
V61
Y62
L63
K64
Y65
R68
R69
D73
P74
R75
P76
E77
Q78
V79
I80
I83
R84
R85
I86
S87
K88
P89
G90
R91
R92
V93
Y94
V95
G96
V97
I100
P101
R102
V103
A110
I111
L112
S113
T114
S115
K116
L119
T120
E123
L127
G130
G131
E132
L133
I134
C135
W138
Molecule 9: 30S ribosomal protein S9
Chain AI:
MET
E2
Q3
Y4 Y5
G6
T7 G8
R9
R10
K11
E12
A13
V14
A15
R16
V17
F18
L19
R20
P21
G22
N23
G24
K25
V26
T27
V28
N29
G30
Q31
D32
F33
N34
E35
Y36
F37
Q38
G39
L40
V41
R42
A43
V44
A45
A46
L47
E48
P49
L50
R51
A52
V53
L56
G57
R58
F59
D60
A61
Y62
I63
T64
V65
K70
S71
G72
Q73
I74
D75
A76
I77
K78
L79
G80
I81
A82
R83
A84
L85
V86
Q87
Y88
N89
P90
D91
Y92
R93
A94
K95
L96
K97
P98
L99
G100
F101
L102
T103
R104
D105
A106
R107
E110
R111
K112
K113
Y114
G115
K116
H117
K118
A119
R120
R121
A122
P123
Q124
Y125
S126
K127
R128
Molecule 9: 30S ribosomal protein S9
Chain CI:
MET
E2
Q3
Y4
Y5
G6
T7
R10
K11
E12
A15
R16
V17
F18
L19
R20
P21
G22
N23
G24
K25
V26
T27
V28
N29
G30
Y36
F37
Q38
G39
L40
V41
R42
A43
V44
A45
A46
L47
E48
P49
L50
V53
D54
A55
R58
F59
D60
A61
Y62
I63
T64
V65
R66
G67
G68
G69
K70
S71
G72
Q73
I74
D75
A76
I77
K78
L79
G80
I81
A82
R83
A84
L85
V86
Q87
Y88
N89
P90
D91
Y92
R93
A94
K95
L96
K97
P98
L99
G100
F101
L102
T103
R104
D105
A106
R107
V108
V109
E110
R111
K112
K113
Y114
G115
K116
H117
K118
A119
R120
R121
A122
P123
Q124
Y125
S126
K127
R128
Molecule 10: 30S ribosomal protein S10
-
Page 30 Full wwPDB X-ray Structure Validation Report 4V7W
Chain AJ:ME
TPR
OK3 I4
R5
I6
K7
L8
R9
G10
F11
D12
H13
K14
T15
L16
D17
A18
S19
A20
Q21
K22
I23
V24
E25
A26
A27
R28
R29
S30
G31
A32
Q33
V34
S35
G36
P37
I38
P39
L40
P41
T42
R43
V44
R45
R46
F47
T48
V49
I50
R51
G52
P53
F54
K55
H56
K57
D58
S59
R60
E61
H62
F63
E64
L65
R66
T67
H68
N69
R70
L71
V72
D73
I74
I75
N76
P77
N78
R79
K80
T81
I82
E83
Q84
L85
M86
T87
L88
D89
L90
P91
V94
E95
I96
E97
I98
K99
T100
V101
GLY
GLY
GLY
ARG
Molecule 10: 30S ribosomal protein S10
Chain CJ:
MET
PRO
K3
I4
R5
I6 K7 L8
R9
G10
F11
D12
H13
K14
T15
L16
D17
A18
S19
A20
Q21
K22
I23
V24
E25
A26
A27
R28
R29
S30
G31
A32
Q33
V34
S35
G36
P37
I38
P39
L40
P41
T42
R43
V44
R45
R46
F47
T48
V49
I50
R51
F54
K55
H56
K57
D58
S59
R60
E61
H62
F63
E64
L65
R66
T67
H68
N69
R70
L71
V72
D73
I74
I75
N76
P77
N78
R79
K80
T81
I82
E83
Q84
L85
M86
T87
L88
D89
L90
P91
V94
E95
I96
E97
I98
K99
T100
V101
GLY
GLY
GLY
ARG
Molecule 11: 30S ribosomal protein S11
Chain AK:
MET
ALA
LYS
LYS
PRO
SER
LYS
LYS
LYS
VAL
K11
R12
Q13
V14
A15
S16
G17
R18
A19
Y20
I21
S24
N27
T28
I29
V30
T31
I32
T33
D34
P35
N38
P39
I40
T41
W42
S43
S44
V47
I48
G49
Y50
K51
G52
K55
G56
T57
P58
Y59
A60
A61
Q62
L63
A64
A65
A68
A69
M73
A74
Y75
G76
M77
V80
D81
V82
I83
V84
R85
G90
R91
E92
Q93
A94
I95
L98
Q99
A100
S101
G102
L103
Q104
V105
K106
S107
I108
V109
D110
D111
T112
P113
V114
N117
G118
C119
R120
P121
K122
K123
K124
F125
R126
K127
A128
S129
Molecule 11: 30S ribosomal protein S11
Chain CK:
MET
ALA
LYS
LYS
PRO
SER
LYS
LYS
LYS
VAL
K11
R12
Q13
V14
A15
R18
A19
Y20
I21
H22
A23
S24
N27
T28
I29
V30
T31
I32
T33
D34
P35
P39
I40
T41
W42
S43
S44
G45
G46
V47
I48
G49
Y50
K51
G52
K55
G56
T57
P58
Y59
A60
A61
Q62
L63
A64
A65
A68
A69
M73
A74
Y75
G76
M77
V80
D81
V82
I83
V84
R85
A89
G90
R91
E92
I95
L98
Q99
A100
S101
G102
L103
Q104
V105
K106
S107
I108
V109
D110
D111
T112
P113
V114
N117
G118
C119
R120
P121
K122
K123
K124
F125
R126
K127
A128
S129
Molecule 12: 30S ribosomal protein S12
Chain AL:
MET
VAL
ALA
LEU
P5 T6 I7 N8 Q9 L10
V11
R12
V18
R19
K20
K21
S22
K23
V24
P25
A26
L27
K28
G29
A30
P31
F32
R33
R34
T38
V39
V40
R41
T42
K46
K47
P48
R53
K54
V55
L60
T61
S62
G63
Y64
E65
V66
T67
A68
Y69
I70
P71
G74
H75
N76
L77
S81
V82
V83
L84
I85
R86
G87
G88
R89
V90
K91
D92
R97
Y98
H99
I100
V101
R102
A108
G109
V110
R113
K114
K115
S116
K119
Y120
K124
P125
K126
E127
A128
A129
LYS
THR
ALA
ALA
LYS
LYS
-
Page 31 Full wwPDB X-ray Structure Validation Report 4V7W
Molecule 12: 30S ribosomal protein S12
Chain CL:
MET
VAL
ALA
LEU
P5 T6 I7 N8 Q9 L10
V11
R12
V18
R19
K20
K21
S22
K23
V24
P25
A26
L27
K28
G29
A30
P31
F32
R33
R34
T38
V39
V40
R41
T42
V43
T44
P45
K46
K47
P48
A51
L52
R53
K54
V55
A56
K57
V58
R59
L60
T61
S62
G63
Y64
E65
V66
T67
A68
Y69
I70
P71
G72
E73
G74
H75
N76
L77
S81
V82
V83
L84
I85
R86
G87
G88
R89
V90
K91
D92
L93
P94
R97
Y98
H99
I100
V101
R102
G103
V104
Y105
A108
G109
V110
K111
D112
R113
K114
K115
K119
Y120
K124
