1M5W

1.96 A Crystal Structure of Pyridoxine 5'-Phosphate Synthase in Complex with 1-deoxy-D-xylulose phosphate

Structural Biology Knowledgebase: 1M5W SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.195

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1M5W

Classification: BIOSYNTHETIC PROTEIN

Total Structure Weight: 212846.58

Macromolecule Entities
Molecule Chains Length Organism Details
Pyridoxal phosphate biosynthetic protein pdxJ A, B, C..., D, E, F, G, HA, B, C, D, E, F, G, H 243 Escherichia coli EC#: 2.6.99.2 IUBMB
Gene Name(s): pdxJ b2564 JW2548

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

A, B, C, E, F, G 1-DEOXY-D-XYLULOSE-5-PHOSPHATE
C5 H11 O7 P
AJPADPZSRRUGHI-RFZPGFLSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, C PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DXP N/A in BindingDB
Kd: 54000 nM  BindingMOAD
Kd: 54000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.195
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 100.01 α = 90.00
b = 129.40 β = 90.00
c = 176.09 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-07-10
  • Released Date: 2003-07-15
  • Deposition author(s): Yeh, J.I., Du, S., Pohl, E., Cane, D.E.

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4