7NOT | pdb_00007not

Crystal structure of Mycobacterium tuberculosis ArgC in complex with nicotinamide adenine dinucleotide phosphate (NADP+) and 5-Methoxy-3-indoleacetic acid

PDB DOI: https://doi.org/10.2210/pdb7NOT/pdb

Classification: OXIDOREDUCTASE
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): Gupta, P., Mendes, V., Blundell, T.L.
Funding Organization(s): Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free:
0.278 (Depositor), 0.273 (DCC)
R-Value Work:
0.202 (Depositor), 0.214 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Models: experimental
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Ligand Structure Quality Assessment

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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

Macromolecule Content

Total Structure Weight: 285.49 kDa
Atom Count: 20,100
Modeled Residue Count: 2,752
Deposited Residue Count: 2,752
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetyl-gamma-glutamyl-phosphate reductase	A, B, C, D, E A, B, C, D, E, F, G, H	344	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: argC, Rv1652, MTCY06H11.17 EC: 1.2.1.38
UniProt
Find proteins for P9WPZ9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPZ9 Go to UniProtKB: P9WPZ9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WPZ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	K [auth C], M [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain K [auth C] Focus chain M [auth D]
MYI (Subject of Investigation/LOI) Query on MYI Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D]	I [auth A], J [auth B], L [auth C], N [auth D]	(5-methoxy-1H-indol-3-yl)acetic acid C₁₁ H₁₁ N O₃ COCNDHOPIHDTHK-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free: 0.278 (Depositor), 0.273 (DCC)
R-Value Work: 0.202 (Depositor), 0.214 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.4	α = 90
b = 132	β = 97.06
c = 124.55	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-06-30

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.