3O15

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.232
R-Value Work: 0.198

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P39594
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3NM Query on 3NM Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-methyl-5-[2-(phosphonooxy)ethyl]-1,3-thiazole-2-carboxylic acid C₇ H₁₀ N O₆ P S XWECMAHAKFWYNV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
POP Query on POP Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PYROPHOSPHATE 2- H₂ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
IFP Query on IFP Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-TRIFLUOROMETHYL-5-METHYLENE-5H-PYRIMIDIN-4-YLIDENEAMINE C₆ H₄ F₃ N₃ YKFRUALXTUDSBW-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.232
R-Value Work: 0.198
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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-07-27

Deposition Author(s):

Revision History (Full details and data files)

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

Prepare Data

Validate Data

Deposit Data

Help and Resources

3O15

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)