3QJA | pdb_00003qja

Crystal Structure of the Mycobacterium tuberculosis Indole-3-glycerol phosphate synthase (TrpC) in apo form

PDB DOI: https://doi.org/10.2210/pdb3QJA/pdb

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

Deposited: 2011-01-28 Released: 2011-06-15
Deposition Author(s): Reddy, M.C.M., Bruning, J.B., Thurman, C., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.29 Å
R-Value Free:
0.181 (Depositor), 0.189 (DCC)
R-Value Work:
0.163 (Depositor), 0.171 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3QJA

This is version 1.3 of the entry. See complete history.

Literature

Small-molecule scaffolds for Mycobacterium tuberculosis Indole Glycerol Phosphate Synthase (IGPS) inhibitors identified by high-throughput screening and defined by X-ray crystallography

Reddy, M.C.M., Bruning, J.B., Thurman, C., Sacchettini, J.C.

To be published.

Macromolecule Content

Total Structure Weight: 28.15 kDa
Atom Count: 2,115
Modeled Residue Count: 254
Deposited Residue Count: 272
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Indole-3-glycerol phosphate synthase	A	272	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: MT1646, MTCY01B2.03, trpC EC: 4.1.1.48
UniProt
Find proteins for P9WFX7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFX7 Go to UniProtKB: P9WFX7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WFX7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.29 Å
R-Value Free: 0.181 (Depositor), 0.189 (DCC)
R-Value Work: 0.163 (Depositor), 0.171 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.069	α = 90
b = 53.505	β = 90
c = 87.826	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-06-15

Deposition Author(s):

Sacchettini, J.C.

TB Structural Genomics Consortium (TBSGC)

Revision History (Full details and data files)

Version 1.0: 2011-06-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.