6SD6 | pdb_00006sd6

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free:
0.236 (Depositor), 0.242 (DCC)
R-Value Work:
0.206 (Depositor), 0.209 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H9P9N5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free: 0.236 (Depositor), 0.242 (DCC)
R-Value Work: 0.206 (Depositor), 0.209 (DCC)
R-Value Observed: 0.208 (Depositor)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-08-26

Deposition Author(s):

Hollingshead, S.

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

Revision History (Full details and data files)

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

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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.