2YZR | pdb_00002yzr

Crystal structure of pyridoxine biosynthesis protein from Methanocaldococcus jannaschii

• PDB DOI: https://doi.org/10.2210/pdb2YZR/pdb

• Classification: LYASE
• Organism(s): Methanocaldococcus jannaschii DSM 2661
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-05-06 Released: 2007-11-06 
• Deposition Author(s): Manzoku, M., Ebihara, A., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.225 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of pyridoxine biosynthesis protein from Methanocaldococcus jannaschii

Manzoku, M., Ebihara, A., Chen, L., Fu, Z.-Q., Chrzas, J., Wang, B.-C., Yokoyama, S., Kuramitsu, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D6  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content 

• Total Structure Weight: 108.01 kDa 
• Atom Count: 7,166 
• Modeled Residue Count: 904 
• Deposited Residue Count: 990 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxal biosynthesis lyase pdxS	A, B, C	330	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0  EC: 4 (PDB Primary Data), 4.3.3.6 (UniProt)
UniProt
Find proteins for Q58090 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58090  Go to UniProtKB:  Q58090

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth C], L [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.225 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.054	α = 90
b = 170.797	β = 90
c = 173.334	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-06 
Deposition Author(s): Manzoku, M., Ebihara, A., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-11-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description