7NN4

Crystal structure of Mycobacterium tuberculosis ArgD with prosthetic group pyridoxal 5'-phosphate and 3-hydroxy-2-naphthoic acid.

• PDB DOI: https://doi.org/10.2210/pdb7NN4/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): Gupta, P., Mendes, V., Blundell, T.L.
• Funding Organization(s): Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.196 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 166.3 kDa 
• Atom Count: 12,855 
• Modelled Residue Count: 1,564 
• Deposited Residue Count: 1,608 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylornithine aminotransferase	A, B, C, D	402	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: argD, Rv1655, MTCY06H11.20 EC: 2.6.1.11
UniProt
Find proteins for P9WPZ7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPZ7  Go to UniProtKB:  P9WPZ7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BZJ (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], I [auth C], J [auth D]	3-hydroxynaphthalene-2-carboxylic acid C11 H8 O3 ALKYHXVLJMQRLQ-UHFFFAOYSA-N
NO3	H [auth C]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B, C, D	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.196 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.19	α = 90
b = 184.35	β = 106.21
c = 71.3	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
xia2	data reduction
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-06-30 
Deposition Author(s): Gupta, P., Mendes, V., 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