4LOM

Crystal Structure of Mycobacterium tuberculosis HisB in complex with its substrate

• PDB DOI: https://doi.org/10.2210/pdb4LOM/pdb

• Classification: LYASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Mycolicibacterium smegmatis
• Mutation(s): No 


• Deposited: 2013-07-13 Released: 2013-08-28 
• Deposition Author(s): Ahangar, M.S., Vyas, R., Nasir, N., Biswal, B.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.249 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 

Literature

Crystal structures of the native, substrate- bound and inhibited forms of Mycobacterium tuberculosis imidazole glycerol phosphate dehydratase

Ahangar, M.S., Vyas, R., Nasir, N., Biswal, B.K.

(2013) Acta Crystallogr D Biol Crystallogr 

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.04 kDa 
• Atom Count: 1,571 
• Modelled Residue Count: 191 
• Deposited Residue Count: 216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Imidazoleglycerol-phosphate dehydratase	A	216	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: hisB, RVBD_1601 EC: 4.2.1.19

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IYP	B [auth A]	(2R,3S)-2,3-dihydroxy-3-(1H-imidazol-5-yl)propyl dihydrogen phosphate C6 H11 N2 O6 P HFYBTHCYPKEDQQ-RITPCOANSA-N
MN	C [auth A], D [auth A], E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.249 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 
• Space Group: P 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.514	α = 90
b = 112.514	β = 90
c = 112.514	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Ahangar, M.S., Vyas, R., Nasir, N., Biswal, B.K.

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2017-06-14
  Changes: Other
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description