3F4N | pdb_00003f4n

Crystal Structure of Pyridoxal Phosphate Biosynthetic Protein PdxJ from Yersinia pestis

• PDB DOI: https://doi.org/10.2210/pdb3F4N/pdb

• Classification: BIOSYNTHETIC PROTEIN, TRANSFERASE
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-11-01 Released: 2008-11-25 
• Deposition Author(s): Kim, Y., Maltseva, N., Stam, J., 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: 2.40 Å
• R-Value Free: 
  0.266 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 5 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 215.1 kDa 
• Atom Count: 15,591 
• Modeled Residue Count: 1,932 
• Deposited Residue Count: 1,968 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxine 5'-phosphate synthase	A, B, C, D, E, F, G, H	246	Yersinia pestis	Mutation(s): 0  Gene Names: pdxJ, y1300, YPO2930, YP_2525 EC: 2.6.99.2
UniProt
Find proteins for Q8ZCP4 (Yersinia pestis) Explore Q8ZCP4  Go to UniProtKB:  Q8ZCP4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PXP	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	L [auth C], O [auth E], P [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.266 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33f4n

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.627	α = 90
b = 114.818	β = 90
c = 154.316	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
BALBES	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-25 
Deposition Author(s): Kim, Y., Maltseva, N., Stam, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• 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