4DV7

Crystal structure of the Thermus thermophilus 30S ribosomal subunit with a 16S rRNA mutation, A915G, bound with streptomycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A structural basis for streptomycin resistance

Demirci, H.Murphy IV, F.Murphy, E.Gregory, S.T.Dahlberg, A.E.Jogl, G.

To be published.

Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S2B256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S3C239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S4D209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S5E162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S6F101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S7G156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S8H138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S9I128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S10J105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S11K129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S12L135Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S13M126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S14N61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S15O89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S16P88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S17Q105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S18R88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S19S93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S20T106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein THXU27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA1522Thermus thermophilus HB8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SRY
Query on SRY

Download Ideal Coordinates CCD File 
V [auth A]STREPTOMYCIN
C21 H39 N7 O12
UCSJYZPVAKXKNQ-HZYVHMACSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
KK [auth D], TK [auth N]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AA [auth A] , AB [auth A] , AC [auth A] , AD [auth A] , AE [auth A] , AF [auth A] , AG [auth A] , AH [auth A] , 
AA [auth A],  AB [auth A],  AC [auth A],  AD [auth A],  AE [auth A],  AF [auth A],  AG [auth A],  AH [auth A],  AI [auth A],  AJ [auth A],  AK [auth A],  AL [auth S],  BA [auth A],  BB [auth A],  BC [auth A],  BD [auth A],  BE [auth A],  BF [auth A],  BG [auth A],  BH [auth A],  BI [auth A],  BJ [auth A],  BK [auth A],  BL [auth T],  CA [auth A],  CB [auth A],  CC [auth A],  CD [auth A],  CE [auth A],  CF [auth A],  CG [auth A],  CH [auth A],  CI [auth A],  CJ [auth A],  CK [auth A],  CL [auth T],  DA [auth A],  DB [auth A],  DC [auth A],  DD [auth A],  DE [auth A],  DF [auth A],  DG [auth A],  DH [auth A],  DI [auth A],  DJ [auth A],  DK [auth A],  DL [auth T],  EA [auth A],  EB [auth A],  EC [auth A],  ED [auth A],  EE [auth A],  EF [auth A],  EG [auth A],  EH [auth A],  EI [auth A],  EJ [auth A],  EK [auth A],  FA [auth A],  FB [auth A],  FC [auth A],  FD [auth A],  FE [auth A],  FF [auth A],  FG [auth A],  FH [auth A],  FI [auth A],  FJ [auth A],  FK [auth A],  GA [auth A],  GB [auth A],  GC [auth A],  GD [auth A],  GE [auth A],  GF [auth A],  GG [auth A],  GH [auth A],  GI [auth A],  GJ [auth A],  GK [auth A],  HA [auth A],  HB [auth A],  HC [auth A],  HD [auth A],  HE [auth A],  HF [auth A],  HG [auth A],  HH [auth A],  HI [auth A],  HJ [auth A],  HK [auth A],  IA [auth A],  IB [auth A],  IC [auth A],  ID [auth A],  IE [auth A],  IF [auth A],  IG [auth A],  IH [auth A],  II [auth A],  IJ [auth A],  IK [auth B],  JA [auth A],  JB [auth A],  JC [auth A],  JD [auth A],  JE [auth A],  JF [auth A],  JG [auth A],  JH [auth A],  JI [auth A],  JJ [auth A],  JK [auth B],  KA [auth A],  KB [auth A],  KC [auth A],  KD [auth A],  KE [auth A],  KF [auth A],  KG [auth A],  KH [auth A],  KI [auth A],  KJ [auth A],  LA [auth A],  LB [auth A],  LC [auth A],  LD [auth A],  LE [auth A],  LF [auth A],  LG [auth A],  LH [auth A],  LI [auth A],  LJ [auth A],  LK [auth D],  MA [auth A],  MB [auth A],  MC [auth A],  MD [auth A],  ME [auth A],  MF [auth A],  MG [auth A],  MH [auth A],  MI [auth A],  MJ [auth A],  MK [auth E],  NA [auth A],  NB [auth A],  NC [auth A],  ND [auth A],  NE [auth A],  NF [auth A],  NG [auth A],  NH [auth A],  NI [auth A],  NJ [auth A],  NK [auth H],  OA [auth A],  OB [auth A],  OC [auth A],  OD [auth A],  OE [auth A],  OF [auth A],  OG [auth A],  OH [auth A],  OI [auth A],  OJ [auth A],  OK [auth H],  PA [auth A],  PB [auth A],  PC [auth A],  PD [auth A],  PE [auth A],  PF [auth A],  PG [auth A],  PH [auth A],  PI [auth A],  PJ [auth A],  PK [auth H],  QA [auth A],  QB [auth A],  QC [auth A],  QD [auth A],  QE [auth A],  QF [auth A],  QG [auth A],  QH [auth A],  QI [auth A],  QJ [auth A],  QK [auth K],  RA [auth A],  RB [auth A],  RC [auth A],  RD [auth A],  RE [auth A],  RF [auth A],  RG [auth A],  RH [auth A],  RI [auth A],  RJ [auth A],  RK [auth M],  SA [auth A],  SB [auth A],  SC [auth A],  SD [auth A],  SE [auth A],  SF [auth A],  SG [auth A],  SH [auth A],  SI [auth A],  SJ [auth A],  SK [auth M],  TA [auth A],  TB [auth A],  TC [auth A],  TD [auth A],  TE [auth A],  TF [auth A],  TG [auth A],  TH [auth A],  TI [auth A],  TJ [auth A],  UA [auth A],  UB [auth A],  UC [auth A],  UD [auth A],  UE [auth A],  UF [auth A],  UG [auth A],  UH [auth A],  UI [auth A],  UJ [auth A],  UK [auth N],  VA [auth A],  VB [auth A],  VC [auth A],  VD [auth A],  VE [auth A],  VF [auth A],  VG [auth A],  VH [auth A],  VI [auth A],  VJ [auth A],  VK [auth N],  W [auth A],  WA [auth A],  WB [auth A],  WC [auth A],  WD [auth A],  WE [auth A],  WF [auth A],  WG [auth A],  WH [auth A],  WI [auth A],  WJ [auth A],  WK [auth P],  X [auth A],  XA [auth A],  XB [auth A],  XC [auth A],  XD [auth A],  XE [auth A],  XF [auth A],  XG [auth A],  XH [auth A],  XI [auth A],  XJ [auth A],  XK [auth P],  Y [auth A],  YA [auth A],  YB [auth A],  YC [auth A],  YD [auth A],  YE [auth A],  YF [auth A],  YG [auth A],  YH [auth A],  YI [auth A],  YJ [auth A],  YK [auth Q],  Z [auth A],  ZA [auth A],  ZB [auth A],  ZC [auth A],  ZD [auth A],  ZE [auth A],  ZF [auth A],  ZG [auth A],  ZH [auth A],  ZI [auth A],  ZJ [auth A],  ZK [auth Q]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
0TD
Query on 0TD
LL-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 403.366α = 90
b = 403.366β = 90
c = 173.597γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-27
    Type: Initial release