4FIR

Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus

Structural Biology Knowledgebase: 4FIR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.185

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4FIR

Classification: lyase

Total Structure Weight: 223774.28

Macromolecule Entities
Molecule Chains Length Organism Details
Pyridoxal biosynthesis lyase pdxS A, B, C..., D, E, FA, B, C, D, E, F 335 Pyrococcus horikoshii EC#: 4.3.3.6 IUBMB
Gene Name(s): pdxS PH1355

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
R5P
Query on R5P

A, B, C, D, E, F RIBOSE-5-PHOSPHATE
C5 H11 O8 P
PPQRONHOSHZGFQ-LMVFSUKVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.185
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 59.17 α = 90.00
b = 179.07 β = 102.53
c = 109.36 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-06-11
  • Released Date: 2012-11-14
  • Deposition author(s): Matsuura, A., Yoon, J.Y., Yoon, H.J., Lee, H.H., Suh, S.W.

Revision History

No revisions since initial release