7E4J | pdb_00007e4j

X-ray crystal structure of VapB12 antitoxin from mycobacterium tuberculosis in space group P41.

PDB DOI: https://doi.org/10.2210/pdb7E4J/pdb

Classification: ANTITOXIN
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2021-02-13 Released: 2022-02-16
Deposition Author(s): Pratap, S., Megta, A.K., Talwar, S., Chandresh, S., Pandey, A.K., Krishnan, V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free:
0.218 (Depositor), 0.243 (DCC)
R-Value Work:
0.172 (Depositor), 0.215 (DCC)
R-Value Observed:
0.174 (Depositor)

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

Literature

X-ray crystal structure of VapB12 antitoxin from mycobacterium tuberculosis in space group P41.

Pratap, S., Megta, A.K., Talwar, S., Sharma, C., Pandey, A.K., Krishnan, V.

To be published.

Macromolecule Content

Total Structure Weight: 19.83 kDa
Atom Count: 1,482
Modeled Residue Count: 176
Deposited Residue Count: 176
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antitoxin	A, B, C, D	44	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: vapB12, AYJ03_009075, DSI38_08650, E5M52_14165, E5M78_13900, ERS007663_00684, ERS007665_03495, ERS007703_02236, ERS007720_02286, ERS007722_03650... vapB12, AYJ03_009075, DSI38_08650, E5M52_14165, E5M78_13900, ERS007663_00684, ERS007665_03495, ERS007703_02236, ERS007720_02286, ERS007722_03650, ERS007741_00752, ERS013471_00074, ERS023446_02694, ERS027646_03040, ERS027659_01239, ERS027661_00782, ERS094182_03044, F6W99_00284, FRD82_02990, SAMEA2683035_01359
UniProt
Find proteins for P9WJ53 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJ53 Go to UniProtKB: P9WJ53
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WJ53
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.218 (Depositor), 0.243 (DCC)
R-Value Work: 0.172 (Depositor), 0.215 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.66	α = 90
b = 34.66	β = 90
c = 162.227	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
SHELXDE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2022-02-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-02-16
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection, 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.