6YJH

Crystal structure of Imidazole Glycerol Phosphate Dehydratase from Mycobacterium tuberculosis at 1.61 A resolution

• PDB DOI: https://doi.org/10.2210/pdb6YJH/pdb

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


• Deposited: 2020-04-03 Released: 2021-04-14 
• Deposition Author(s): Timofeev, V.I., Abramchik, Y.A., Skvortsov, T.A., Azhikina, T.L., Muravieva, T.I., Kostromina, M.A., Esipov, R.S., Kuranova, I.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.175 
• R-Value Work: 0.151 
• R-Value Observed: 0.152 

Starting Model: experimental

Literature

Crystal structure of Imidazole Glycerol Phosphate Dehydratase from Mycobacterium tuberculosis at 1.61 A resolution

Timofeev, V.I., Abramchik, Y.A., Skvortsov, T.A., Azhikina, T.L., Muravieva, T.I., Kostromina, M.A., Esipov, R.S., Kuranova, I.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 23-mer - A23 

Local Symmetry: Cyclic - C4  (Explore in 3D)
Local Stoichiometry: Homo 20-mer - A20 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 21.14 kDa 
• Atom Count: 1,613 
• Modelled Residue Count: 191 
• Deposited Residue Count: 191 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Imidazoleglycerol-phosphate dehydratase	A	191	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for P9WML9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WML9  Go to UniProtKB:  P9WML9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	B [auth A], C [auth A], D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.175 
• R-Value Work: 0.151 
• R-Value Observed: 0.152 
• Space Group: P 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.13	α = 90
b = 112.13	β = 90
c = 112.13	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-14 
Deposition Author(s): Timofeev, V.I., Abramchik, Y.A., Skvortsov, T.A., Azhikina, T.L., Muravieva, T.I., Kostromina, M.A., Esipov, R.S., Kuranova, I.P.

Revision History  

• Version 1.0: 2021-04-14
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description