7NOR

Crystal structure of Mycobacterium tuberculosis ArgF in complex with 2-fluoro-4-hydroxybenzonitrile.

• PDB DOI:  https://doi.org/10.2210/pdb7NOR/pdb

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


• Deposited: 2021-02-25 Released: 2021-06-30 
• Deposition Author(s): Mendes, V., Gupta, P., Burgess, A., Sebastian-Perez, V., Cattermole, E., Meghir, C., Blundell, T.L.
• Funding Organization(s): Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.186 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

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: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 200.75 kDa 
• Atom Count: 15,246 
• Modelled Residue Count: 1,810 
• Deposited Residue Count: 1,854 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ornithine carbamoyltransferase	A, B, C, D, E, F	309	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: argF, Rv1656, MTCY06H11.21 EC: 2.1.3.3
UniProt
Find proteins for P9WIT9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WIT9  Go to UniProtKB:  P9WIT9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8H8 (Subject of Investigation/LOI)	K [auth A], L [auth A], P [auth D], S [auth E]	2-fluoro-4-hydroxybenzonitrile C7 H4 F N O REIVHYDACHXPNH-UHFFFAOYSA-N
PO4	G [auth A], H [auth A], I [auth A], J [auth A], M [auth C], N [auth C], O [auth D], Q [auth E], R [auth E], T [auth F]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.186 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.453	α = 90
b = 142.734	β = 117.5
c = 97.697	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-06-30 
Deposition Author(s): Mendes, V., Gupta, P., Burgess, A., Sebastian-Perez, V., Cattermole, E., Meghir, C., 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