4KVB | pdb_00004kvb

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 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 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.

Macromolecule Content 

  • Total Structure Weight: 776.9 kDa 
  • Atom Count: 51,128 
  • Modeled Residue Count: 3,807 
  • Deposited Residue Count: 3,957 
  • Unique protein chains: 19
  • Unique nucleic acid chains: 1

Macromolecules


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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S2256Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for P62662 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S3239Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for P62663 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S4209Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for P62664 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S5162Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for P62665 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S6101Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for P62666 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S7156Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for P62667 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S8138Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for P62668 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S9128Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for P62669 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S10105Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for P62653 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S11129Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S12134Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for P61941 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S13126Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for P62655 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type Z61Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for P62656 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S1589Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for P62657 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S1688Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for P62238 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S18Q [auth R]88Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for P62659 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S19R [auth S]93Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S20S [auth T]106Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein ThxT [auth U]27Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNA1,522Thermus thermophilus HB27
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN


Download:Ideal Coordinates CCD File
AH [auth D],
FH [auth N]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K

Query on K


Download:Ideal Coordinates CCD File
AG [auth A]
BG [auth A]
CG [auth A]
DG [auth A]
EG [auth A]
AG [auth A],
BG [auth A],
CG [auth A],
DG [auth A],
EG [auth A],
FG [auth A],
GG [auth A],
HG [auth A],
IG [auth A],
JG [auth A],
KG [auth A],
LG [auth A],
MG [auth A],
NG [auth A],
OG [auth A],
PF [auth A],
PG [auth A],
QF [auth A],
QG [auth A],
RF [auth A],
RG [auth A],
SF [auth A],
SG [auth A],
TF [auth A],
TG [auth A],
UF [auth A],
UG [auth A],
VF [auth A],
VG [auth A],
WF [auth A],
WG [auth A],
XF [auth A],
XG [auth A],
YF [auth A],
ZF [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
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],
BA [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
BH [auth D],
CA [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
CH [auth E],
DA [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
DH [auth E],
EA [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
EH [auth M],
FA [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
GA [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
GH [auth U],
HA [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
IA [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
JA [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
KA [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
PA [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
QA [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
RA [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
SA [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
U [auth A],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
V [auth A],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
W [auth A],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
X [auth A],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
Y [auth A],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
YG [auth A],
Z [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZG [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
0TD
Query on 0TD
L
L-PEPTIDE LINKINGC5 H9 N O4 SASP

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free:  0.258 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
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

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-04
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-12-06
    Changes: Data collection
  • Version 1.4: 2025-02-19
    Changes: Data collection, Structure summary