4DUY

Crystal structure of the Thermus thermophilus 30S ribosomal subunit with a 16S rRNA mutation, U13C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.39 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

wwPDB Validation 3D Report Full Report



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

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S4
D
209Thermus thermophilusMutation(s): 0 
Gene Names: rpsDrps4TTHA1665
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80373

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S5
E
162Thermus thermophilusMutation(s): 0 
Gene Names: rpsETTHA1675
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ5

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S6
F
101Thermus thermophilusMutation(s): 0 
Gene Names: rpsFTTHA0245
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP8

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S7
G
156Thermus thermophilusMutation(s): 0 
Gene Names: rpsGrps7TTHA1696
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P17291

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S9
I
128Thermus thermophilusMutation(s): 0 
Gene Names: rpsIrps9TTHA1464
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80374

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S10
J
105Thermus thermophilusMutation(s): 0 
Gene Names: rpsJTTHA1693
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN7

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S11
K
129Thermus thermophilusMutation(s): 0 
Gene Names: rpsKrps11TTHA1666
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80376

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S14
N
61Thermus thermophilusMutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY6

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S19
S
93Thermus thermophilusMutation(s): 0 
Gene Names: rpsSTTHA1688
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP2

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein THX
U
27Thermus thermophilusMutation(s): 0 
Gene Names: rpsUTTHA1396
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIH3

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S12
L
135Thermus thermophilusMutation(s): 0 
Find proteins for F6DEQ7 (Thermus thermophilus (strain SG0.5JP17-16))
Go to UniProtKB:  F6DEQ7

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S13
M
126Thermus thermophilusMutation(s): 0 
Gene Names: rpsMrps13TTHA1667
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80377

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S15
O
89Thermus thermophilusMutation(s): 0 
Gene Names: rpsOTTHA1138
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJ76

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S16
P
88Thermus thermophilusMutation(s): 0 
Gene Names: rpsPTTHA1035
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJH3

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S17
Q
105Thermus thermophilusMutation(s): 0 
Gene Names: rpsQTTHA1683
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY7

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S18
R
88Thermus thermophilusMutation(s): 0 
Gene Names: rpsRTTHA0243
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ0

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S2
B
256Thermus thermophilusMutation(s): 0 
Gene Names: rpsBrps2TTHA0861
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80371

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S20
T
106Thermus thermophilusMutation(s): 0 
Gene Names: rpsTrps20TTHA1397
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80380

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S3
C
239Thermus thermophilusMutation(s): 0 
Gene Names: rpsCrps3TTHA1686
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80372

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S8
H
138Thermus thermophilusMutation(s): 0 
Gene Names: rpsHTTHA1678
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY9

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Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAA1522Thermus thermophilus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
D, N
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C, D, E, F, G, J, N, P, Q, S
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: 3.39 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 402.518α = 90
b = 402.518β = 90
c = 175.892γ = 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 

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