4KVB

Thermus thermophilus HB27 30S ribosomal subunit lacking ribosomal protein S17


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.198 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.217 

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

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
B
256Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsB (rps2)
Find proteins for P62662 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62662
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
C
239Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsC (rps3)
Find proteins for P62663 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62663
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
D
209Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsD (rps4)
Find proteins for P62664 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62664
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
E
162Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsE (rps5)
Find proteins for P62665 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62665
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
F
101Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsF (rps6)
Find proteins for P62666 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62666
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
G
156Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsG (rps7)
Find proteins for P62667 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62667
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
H
138Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsH (rps8)
Find proteins for P62668 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62668
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
I
128Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsI (rps9)
Find proteins for P62669 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62669
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
J
105Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsJ (rps10)
Find proteins for P62653 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62653
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
K
129Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsK (rps11)
Find proteins for P62654 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62654
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
L
134Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsL (rps12)
Find proteins for P61941 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P61941
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
M
126Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsM (rps13)
Find proteins for P62655 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62655
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
N
61Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsZ (rps14, rpsN)
Find proteins for P62656 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62656
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
O
89Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsO (rps15)
Find proteins for P62657 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62657
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
P
88Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsP (rps16)
Find proteins for P62238 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62238
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
R
88Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsR (rps18)
Find proteins for P62659 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62659
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
S
93Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsS (rps19)
Find proteins for P62660 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62660
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
T
106Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsT (rps20)
Find proteins for P62661 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62661
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
U
27Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsU
Find proteins for P62613 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62613
Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAA1522Thermus thermophilus HB27
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A, B, D, E, M, U
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  9 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
A
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
A
RNA LINKINGC10 H16 N3 O8 PC
M2G
Query on M2G
A
RNA LINKINGC12 H18 N5 O8 PG
MA6
Query on MA6
A
RNA LINKINGC12 H18 N5 O7 PA
2MG
Query on 2MG
A
RNA LINKINGC11 H16 N5 O8 PG
UR3
Query on UR3
A
RNA LINKINGC10 H15 N2 O9 PU
7MG
Query on 7MG
A
RNA LINKINGC11 H18 N5 O8 PG
0TD
Query on 0TD
L
L-PEPTIDE LINKINGC5 H9 N O4 SASP
4OC
Query on 4OC
A
RNA LINKINGC11 H18 N3 O8 PC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.198 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.217 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 397.316α = 90.00
b = 397.316β = 90.00
c = 215.505γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
CBASSdata collection
DENZOdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Refinement description