7NN8

Crystal structure of Mycobacterium tuberculosis ArgB in complex with 1H-indole-3-carbonitrile.

• PDB DOI: https://doi.org/10.2210/pdb7NN8/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-02-24 Released: 2021-06-30 
• Deposition Author(s): Mendes, V., Thomas, S.E., Cory-Wright, J., Blundell, T.L.
• Funding Organization(s): Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.233 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Starting Model: experimental

Literature

A fragment-based approach to assess the ligandability of ArgB, ArgC, ArgD and ArgF in the L-arginine biosynthetic pathway of Mycobacterium tuberculosis

Gupta, P., Thomas, S.E., Zaidan, S.A., Pasillas, M.A., Cory-Wright, J., Sebastian-Perez, V., Burgess, A., Cattermole, E., Meghir, C., Abell, C., Coyne, A.G., Jacobs, W.R., Blundell, T.L., Tiwari, S., Mendes, V.

(2021) Comput Struct Biotechnol J 19: 3491-3506

• DOI: https://doi.org/10.1016/j.csbj.2021.06.006

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 31.61 kDa 
• Atom Count: 2,142 
• Modelled Residue Count: 291 
• Deposited Residue Count: 297 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylglutamate kinase	A	297	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: argB, Rv1654, MTCY06H11.19 EC: 2.7.2.8
UniProt
Find proteins for P9WQ01 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WQ01  Go to UniProtKB:  P9WQ01

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
98Z (Subject of Investigation/LOI)	D [auth A]	1~{H}-indole-3-carbonitrile C9 H6 N2 CHIFTAQVXHNVRW-UHFFFAOYSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.233 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.647	α = 90
b = 174.647	β = 90
c = 72.118	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-06-30 
Deposition Author(s): Mendes, V., Thomas, S.E., Cory-Wright, J., Blundell, T.L.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	OPP1158806

Revision History  

• Version 1.0: 2021-06-30
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description