6JQY

Crystal structure of N-terminal domain of VapB46 antitoxin from Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb6JQY/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Mycobacterium tuberculosis CDC1551
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-04-02 Released: 2020-04-08
Deposition Author(s): Roy, M., Singh, B.K., Bhattacharyya, S., Das, A.K.
Funding Organization(s): Department of Biotechnology (India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free: 0.232
R-Value Work: 0.195
R-Value Observed: 0.197

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of N-terminal domain of VapB46 antitoxin from Mycobacterium tuberculosis

Roy, M., Singh, B.K., Bhattacharyya, S., Das, A.k.

To be published.

Macromolecule Content

Total Structure Weight: 19.41 kDa
Atom Count: 1,401
Modelled Residue Count: 174
Deposited Residue Count: 176
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antitoxin VapB46	A, B, C, D	44	Mycobacterium tuberculosis CDC1551	Mutation(s): 1 Gene Names: vapB46, MT3493
UniProt
Find proteins for P9WF13 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WF13 Go to UniProtKB: P9WF13
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WF13
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth D]	E [auth A], F [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free: 0.232
R-Value Work: 0.195
R-Value Observed: 0.197
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.043	α = 90
b = 50.548	β = 116.13
c = 42.623	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-04-08

Deposition Author(s):

Bhattacharyya, S.

Funding Organization	Location	Grant Number
Department of Biotechnology (India)	India	BT/PR12404/BRB/10/1362/ 2014

Revision History (Full details and data files)

Version 1.0: 2020-04-08
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.