7E4J

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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.218 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

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.

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: homology

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: 19.83 kDa 
• Atom Count: 1,482 
• Modelled Residue Count: 176 
• Deposited Residue Count: 176 
• Unique protein chains: 1

Macromolecules

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, 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.218 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• 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

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2022-02-16
  Type: Initial release