Macromolecule Content

Total Structure Weight: 130.25 kDa
Atom Count: 8972
Modelled Residue Count: 1094
Deposited 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 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.210
R-Value Work: 0.194
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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:

(by identity cutoff) | Structure

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, TTHA0704 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
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] MOL2 format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.210
R-Value Work: 0.194
R-Value Observed: 0.194
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

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2007-10-29
Released Date: 2007-12-18

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-12-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.