3F4N

Crystal Structure of Pyridoxal Phosphate Biosynthetic Protein PdxJ from Yersinia pestis

Structural Biology Knowledgebase: 3F4N SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.191

Literature

Macromolecules
Sequence Display for 3F4N

Classification: BIOSYNTHETIC PROTEIN TRANSFERASE

Total Structure Weight: 215103.61

Macromolecule Entities
Molecule Chains Length Organism Details
Pyridoxine 5'-phosphate synthase A, B, C..., D, E, F, G, HA, B, C, D, E, F, G, H 246 Yersinia pestis EC#: 2.6.99.2 IUBMB
Gene Name(s): pdxJ YPO2930 y1300 YP_2525
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PXP
Query on PXP

A, B, C, D, E, F, G, H PYRIDOXINE-5'-PHOSPHATE
C8 H12 N O6 P
WHOMFKWHIQZTHY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

C, E SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 113.63 α = 90.00
b = 114.82 β = 90.00
c = 154.32 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-11-01
  • 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

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Refinement description | Details: Fixed TLS group
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4