4DV0

Crystal structure of the Thermus thermophilus 30S ribosomal subunit with a 16S rRNA mutation, U20G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.85 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.150 

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
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S3C239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S4D209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S5E162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
UniProt
Find proteins for Q5SHQ5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S6F101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
UniProt
Find proteins for Q5SLP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S7G156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
UniProt
Find proteins for P17291 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S8H138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
UniProt
Find proteins for P0DOY9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S9I128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S10J105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
UniProt
Find proteins for Q5SHN7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S11K129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
UniProt
Find proteins for P80376 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S12L135Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
UniProt
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S13M126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
UniProt
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S14N61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
UniProt
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S15O89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
UniProt
Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S16P88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S17Q105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
UniProt
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S18R88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S19S93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S20T106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein THXU27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA1,522Thermus thermophilus HB8
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
AA [auth A],
AB [auth A],
AC [auth A],
AD [auth A],
AE [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 C],
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],
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 D],
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 D],
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 E],
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 F],
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 J],
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 J],
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 M],
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],
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],
KK [auth P],
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 P],
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 Q],
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 S],
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],
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],
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],
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],
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],
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],
V [auth A],
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],
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],
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 B],
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 B],
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 B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
0TD
Query on 0TD
L L-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.85 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.150 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 402.108α = 90
b = 402.108β = 90
c = 173.997γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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