Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 130250.84 
• Atom Count: 8350 
• Residue Count: 1188 
• Unique protein chains: 1

2ZBT

Crystal structure of pyridoxine biosynthesis protein from Thermus thermophilus HB8

• DOI: 10.2210/pdb2ZBT/pdb

• Classification: LYASE
• Organism(s): Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
• Expression System: Escherichia coli BL21(DE3)


• 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 
• R-Value Work: 0.194 

Literature

Crystal structure of pyridoxine biosynthesis protein from Thermus thermophilus HB8

Manzoku, M., Ebihara, A., Fujimoto, Y., Yokoyama, S., Kuramitsu, S.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MPD	A, B, C, 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 
• R-Value Work: 0.194 
• Space Group: H 3

Unit Cell:

Length (Å)	Angle (°)
a = 180.970	α = 90.00
b = 180.970	β = 90.00
c = 100.750	γ = 120.00

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

• Deposited Date: 2007-10-29 
• 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
  Type: Source and taxonomy, Version format compliance