6SD6

Structure of VapBC from Shigella sonnei

• PDB DOI: https://doi.org/10.2210/pdb6SD6/pdb

• Classification: TOXIN
• Organism(s): Shigella sonnei
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-07-26 Released: 2020-08-26 
• Deposition Author(s): Lea, S.M., Hollingshead, S.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.236 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Literature

Polymorphisms in the VapBC toxin:antitoxin system mediate high frequency plasmid loss in Shigella sonnei

Martyn, J.E., Pilla, G., Hollingshead, S., Lea, S.M., McVicker, G., Tang, C.M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 8-mer - A4B2C2 

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

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content

• Total Structure Weight: 51.16 kDa 
• Atom Count: 3,191 
• Modelled Residue Count: 402 
• Deposited Residue Count: 454 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antitoxin	A, B	75	Shigella sonnei	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA(fMet)-specific endonuclease VapC	C, D	152	Shigella sonnei	Mutation(s): 0  Gene Names: vapC, BZ172_30265 EC: 3.1
UniProt
Find proteins for A0A0H9P9N5 (Shigella sonnei) Explore A0A0H9P9N5  Go to UniProtKB:  A0A0H9P9N5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.236 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.873	α = 90
b = 95.873	β = 90
c = 116.389	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-26 
Deposition Author(s): Lea, S.M., Hollingshead, S.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	102908/Z/13/Z

Revision History  

• Version 1.0: 2020-08-26
  Type: Initial release
  
• Version 1.1: 2020-09-02
  Changes: Structure summary
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description