4KVB

Thermus thermophilus HB27 30S ribosomal subunit lacking ribosomal protein S17


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural robustness of the ribosome inferred from the X-ray crystal structure of a 30S ribosomal subunit lacking ribosomal protein S17

Connetti, J.L.Murphy, E.L.Dahlberg, A.E.Gregory, S.T.Jogl, G.

To be published.

Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2 B256Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsBrps2TT_C0509
Find proteins for P62662 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3 C239Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsCrps3TT_C1322
Find proteins for P62663 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4 D209Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsDrps4TT_C1301
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5 E162Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsErps5TT_C1311
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6 F101Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsFrps6TT_C1740
Find proteins for P62666 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7 G156Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsGrps7TT_C1332
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8 H138Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsHrps8TT_C1314
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9 I128Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsIrps9TT_C1100
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10 J105Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsJrps10TT_C1329
Find proteins for P62653 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11 K129Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsKrps11TT_C1302
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12 L134Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsLrps12TT_C1333
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13 M126Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsMrps13TT_C1303
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type Z N61Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsZrps14rpsNTT_C1315
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15 O89Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsOrps15TT_C0773
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16 P88Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsPrps16TT_C0673
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18 R88Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsRrps18TT_C1742
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19 S93Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsSrps19TT_C1324
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20 T106Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsTrps20TT_C1031
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein Thx U27Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsUTT_C1030
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA1522Thermus thermophilus HB27
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A, B, D, E, M, U
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: 4.20 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 397.316α = 90
b = 397.316β = 90
c = 215.505γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
CBASSdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2013-05-22 
  • Released Date: 2014-06-04 
  • Deposition Author(s): Murphy, E.L., Jogl, G.

Revision History 

  • Version 1.0: 2014-06-04
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description