3O15 | pdb_00003o15

Crystal Structure of Bacillus subtilis Thiamin Phosphate Synthase Complexed with a Carboxylated Thiazole Phosphate

• PDB DOI: https://doi.org/10.2210/pdb3O15/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-07-20 Released: 2011-07-27 
• Deposition Author(s): McCulloch, K.M., Hanes, J.W., Abdelwahed, S., Mahanta, N., Hazra, A., Ishida, K., Begley, T.P., Ealick, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.232 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.197 (DCC) 

Literature

Crystal Structure and Kinetic Characterization of Bacillus subtilis Thiamin Phosphate Synthase with a Carboxylated Thiazole Phosphate

McCulloch, K.M., Hanes, J.W., Abdelwahed, S., Mahanta, N., Hazra, A., Ishida, K., Begley, T.P., Ealick, S.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 25.92 kDa 
• Atom Count: 1,884 
• Modeled Residue Count: 219 
• Deposited Residue Count: 235 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiamine-phosphate pyrophosphorylase	A	235	Bacillus subtilis	Mutation(s): 0  Gene Names: thiE EC: 2.5.1.3
UniProt
Find proteins for P39594 (Bacillus subtilis (strain 168)) Explore P39594  Go to UniProtKB:  P39594

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3NM	B [auth A]	4-methyl-5-[2-(phosphonooxy)ethyl]-1,3-thiazole-2-carboxylic acid C7 H10 N O6 P S XWECMAHAKFWYNV-UHFFFAOYSA-N
POP	D [auth A]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
IFP	C [auth A]	2-TRIFLUOROMETHYL-5-METHYLENE-5H-PYRIMIDIN-4-YLIDENEAMINE C6 H4 F3 N3 YKFRUALXTUDSBW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.232 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.197 (DCC) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.02	α = 90
b = 96.02	β = 90
c = 59.34	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-27 
Deposition Author(s): McCulloch, K.M., Hanes, J.W., Abdelwahed, S., Mahanta, N., Hazra, A., Ishida, K., Begley, T.P., Ealick, S.E.

Revision History  

• Version 1.0: 2011-07-27
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations