3F4N

Crystal Structure of Pyridoxal Phosphate Biosynthetic Protein PdxJ from Yersinia pestis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.195 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of Pyridoxal Phosphate Biosynthetic Protein PdxJ from Yersinia pestis

Kim, Y.Maltseva, N.Stam, J.Anderson, W.F.Joachimiak, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyridoxine 5'-phosphate synthase
A, B, C, D, E
A, B, C, D, E, F, G, H
246Yersinia pestisMutation(s): 0 
Gene Names: pdxJy1300YPO2930YP_2525
EC: 2.6.99.2
UniProt
Find proteins for Q8ZCP4 (Yersinia pestis)
Explore Q8ZCP4 
Go to UniProtKB:  Q8ZCP4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZCP4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PXP
Query on PXP

Download Ideal Coordinates CCD File 
I [auth A]
J [auth B]
K [auth C]
M [auth D]
N [auth E]
I [auth A],
J [auth B],
K [auth C],
M [auth D],
N [auth E],
Q [auth F],
R [auth G],
S [auth H]
PYRIDOXINE-5'-PHOSPHATE
C8 H12 N O6 P
WHOMFKWHIQZTHY-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
L [auth C],
O [auth E],
P [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.627α = 90
b = 114.818β = 90
c = 154.316γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
HKL-3000data collection
BALBESphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description