3O6D

Pyridoxal phosphate biosynthetic protein PdxJ from Campylobacter jejuni in complex with pyridoxine-5'-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray crystal structure of pyridoxal phosphate biosynthetic protein PdxJ from Campylobacter jejuni.

Osipiuk, J.Zhou, M.Kwon, K.Anderson, W.F.Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyridoxine 5'-phosphate synthase
A
260Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)Gene Names: pdxJ
EC: 2.6.99.2
Find proteins for Q9PN59 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168))
Go to UniProtKB:  Q9PN59
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
PXP
Query on PXP

Download SDF File 
Download CCD File 
A
PYRIDOXINE-5'-PHOSPHATE
C8 H12 N O6 P
WHOMFKWHIQZTHY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 90.239α = 90.00
b = 90.239β = 90.00
c = 156.081γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
SBC-Collectdata collection
DENZOdata reduction
HKL-3000data scaling
MLPHAREphasing
SHELXDphasing
PDB_EXTRACTdata extraction
REFMACrefinement
HKL-3000phasing
SCALEPACKdata scaling
DMphasing
RESOLVEphasing
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description