3T55 | pdb_00003t55

Crystal structure of Mycobacterium tuberculosis Indole Glycerol Phosphate Synthase (IGPS) in complex with Phenoxymethyl Benzoic Acid (PMBA)

• PDB DOI: https://doi.org/10.2210/pdb3T55/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-07-26 Released: 2012-08-08 
• Deposition Author(s): Reddy, M.C.M., Bruning, J.B., Thurman, C., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Structural Insights and Inhibition of Mycobacterium tuberculosis Indole Glycerol Phosphate Synthase (IGPS): an Essential Enzyme for Tryptophan Biosynthesis

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

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: 28.48 kDa 
• Atom Count: 2,040 
• Modeled Residue Count: 258 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

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, Rv1611, trpC EC: 4.1.1.48
UniProt
Find proteins for P9WFX7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFX7  Go to UniProtKB:  P9WFX7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4RG	B [auth A]	3-(phenoxymethyl)benzoic acid C14 H12 O3 URLYREZIPSJJQU-UHFFFAOYSA-N
MLI	C [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.838	α = 90
b = 53.206	β = 90
c = 87.167	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-08 
Deposition Author(s): Reddy, M.C.M., Bruning, J.B., Thurman, C., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)

Revision History  

• Version 1.0: 2012-08-08
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description