3O6D | pdb_00003o6d

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

• PDB DOI: https://doi.org/10.2210/pdb3O6D/pdb

• Classification: TRANSFERASE
• Organism(s): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-07-28 Released: 2010-08-11 
• Deposition Author(s): Osipiuk, J., Zhou, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.197 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.91 kDa 
• Atom Count: 2,285 
• Modeled Residue Count: 259 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxine 5'-phosphate synthase	A	260	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	Mutation(s): 0  Gene Names: Cj1238, pdxJ EC: 2.6.99.2
UniProt
Find proteins for Q9PN59 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q9PN59  Go to UniProtKB:  Q9PN59

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PXP	B [auth A]	PYRIDOXINE-5'-PHOSPHATE C8 H12 N O6 P WHOMFKWHIQZTHY-UHFFFAOYSA-N
PO4	C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.197 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33o6d

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.239	α = 90
b = 90.239	β = 90
c = 156.081	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-11 
Deposition Author(s): Osipiuk, J., Zhou, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2010-08-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary