2ZBT | pdb_00002zbt

Crystal structure of pyridoxine biosynthesis protein from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb2ZBT/pdb

• Classification: LYASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-10-29 Released: 2007-12-18 
• Deposition Author(s): Manzoku, M., Ebihara, A., Fujimoto, Y., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Crystal structure of pyridoxine biosynthesis protein from Thermus thermophilus HB8

Manzoku, M., Ebihara, A., Fujimoto, Y., 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: 130.25 kDa 
• Atom Count: 8,972 
• Modeled Residue Count: 1,094 
• Deposited Residue Count: 1,188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxal biosynthesis lyase pdxS	A, B, C, D	297	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: pdxS EC: 4 (PDB Primary Data), 4.3.3.6 (UniProt)
UniProt
Find proteins for Q5SKD9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKD9  Go to UniProtKB:  Q5SKD9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	E [auth A], F [auth B], G [auth C], H [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.97	α = 90
b = 180.97	β = 90
c = 100.75	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-18 
Deposition Author(s): Manzoku, M., Ebihara, A., Fujimoto, Y., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-12-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations