3O63 | pdb_00003o63

Crystal Structure of Thiamin Phosphate Synthase from Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb3O63/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-07-28 Released: 2011-07-27
Deposition Author(s): McCulloch, K.M., Ramamoorthy, D., Ishida, K., Guida, W.C., Begley, T.P., Ealick, S.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.264 (Depositor), 0.263 (DCC)
R-Value Work:
0.207 (Depositor), 0.207 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3O63

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

Literature

Crystal Structure and Identification of Potential Inhibitor Compounds for Mycobacterium tuberculosis Thiamin Phosphate Synthase

McCulloch, K.M., Ramamoorthy, D., Ishida, K., Guida, W.C., Begley, T.P., Ealick, S.E.

To be published.

Macromolecule Content

Total Structure Weight: 51.62 kDa
Atom Count: 3,264
Modeled Residue Count: 424
Deposited Residue Count: 486
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable thiamine-phosphate pyrophosphorylase	A, B	243	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: MT0427, MTCY22G10.11c, Rv0414c, thiE EC: 2.5.1.3
UniProt
Find proteins for P9WG75 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WG75 Go to UniProtKB: P9WG75
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WG75
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.264 (Depositor), 0.263 (DCC)
R-Value Work: 0.207 (Depositor), 0.207 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.61	α = 90
b = 91.37	β = 90
c = 124.62	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-07-27

Deposition Author(s):

McCulloch, K.M.

Ramamoorthy, D.

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.