5D8H | pdb_00005d8h

CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.245 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.208 (Depositor) 
  • R-Value Observed: 
    0.210 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5D8H

This is version 2.1 of the entry. See complete history. 

Literature

CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON

Gabdulkhakov, A.G., Mitroshin, I.V., Garber, M.B.

To be published.

Macromolecule Content 

  • Total Structure Weight: 67.89 kDa 
  • Atom Count: 4,592 
  • Modeled Residue Count: 458 
  • Deposited Residue Count: 467 
  • Unique protein chains: 3
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L10213Methanocaldococcus jannaschiiMutation(s): 1 
Gene Names: rpl10, rplP0, MJ0509
UniProt
Find proteins for P54049 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore P54049 
Go to UniProtKB:  P54049
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54049
Sequence Annotations
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L11161Methanocaldococcus jannaschiiMutation(s): 0 
Gene Names: rpl11, MJ0373
UniProt
Find proteins for P54030 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore P54030 
Go to UniProtKB:  P54030
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54030
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
THIOSTREPTON19Streptomyces azureusMutation(s): 0 
UniProt
Find proteins for P0C8P8 (Streptomyces azureus)
Explore P0C8P8 
Go to UniProtKB:  P0C8P8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C8P8
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff) 
Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal RNA74Methanocaldococcus jannaschii
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on TRS


Download:Ideal Coordinates CCD File
R [auth A],
S [auth A],
U [auth B]		2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
MG

Query on MG


Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
V [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA

Query on NA


Download:Ideal Coordinates CCD File
O [auth A],
P [auth A],
Q [auth A],
T [auth B]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  6 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
BB9
Query on BB9
D
PEPTIDE LINKINGC3 H5 N O2 SCYS
DBU
Query on DBU
D
PEPTIDE LINKINGC4 H7 N O2THR
DCY
Query on DCY
D
D-PEPTIDE LINKINGC3 H7 N O2 S

--

DHA
Query on DHA
D
PEPTIDE LINKINGC3 H5 N O2SER
MH6
Query on MH6
D
PEPTIDE LINKINGC3 H5 N O3SER
TS9
Query on TS9
D
L-PEPTIDE LINKINGC6 H13 N O4ILE

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.245 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.208 (Depositor) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.07α = 90
b = 127.16β = 90
c = 132.93γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2016-12-14
    Changes: Structure summary
  • Version 1.2: 2016-12-21
    Changes: Non-polymer description
  • Version 1.3: 2019-04-10
    Changes: Advisory, Data collection, Database references
  • Version 2.0: 2019-04-24
    Changes: Data collection, Polymer sequence
  • Version 2.1: 2025-04-09
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary