3JTJ | pdb_00003jtj

3-deoxy-manno-octulosonate cytidylyltransferase from Yersinia pestis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 
    0.209 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

X-ray crystal structure of 3-deoxy-manno-octulosonate cytidylyltransferase from Yersinia pestis.

Osipiuk, J.Zhou, M.Grimshaw, S.Anderson, W.F.Joachimiak, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-deoxy-manno-octulosonate cytidylyltransferase253Yersinia pestis CO92Mutation(s): 0 
Gene Names: kdsBy2772YPO1400YP_1193
EC: 2.7.7.38
UniProt
Find proteins for Q8ZGA4 (Yersinia pestis)
Explore Q8ZGA4 
Go to UniProtKB:  Q8ZGA4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZGA4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free:  0.209 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.058α = 90
b = 97.058β = 90
c = 93.626γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary