Vibrio cholerae ParD2 Antitoxin

Experimental Data Snapshot

  • Resolution: 3.08 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.272 

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Entropic pressure controls the oligomerization of the Vibrio cholerae ParD2 antitoxin.

Garcia-Rodriguez, G.Girardin, Y.Volkov, A.N.Singh, R.K.Muruganandam, G.Van Dyck, J.Sobott, F.Versees, W.Charlier, D.Loris, R.

(2021) Acta Crystallogr D Struct Biol 77: 904-920

  • DOI: https://doi.org/10.1107/S2059798321004873
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    ParD2 is the antitoxin component of the parDE2 toxin-antitoxin module from Vibrio cholerae and consists of an ordered DNA-binding domain followed by an intrinsically disordered ParE-neutralizing domain. In the absence of the C-terminal intrinsically disordered protein (IDP) domain, V. cholerae ParD2 (VcParD2) crystallizes as a doughnut-shaped hexadecamer formed by the association of eight dimers. This assembly is stabilized via hydrogen bonds and salt bridges rather than by hydrophobic contacts. In solution, oligomerization of the full-length protein is restricted to a stable, open decamer or dodecamer, which is likely to be a consequence of entropic pressure from the IDP tails. The relative positioning of successive VcParD2 dimers mimics the arrangement of Streptococcus agalactiae CopG dimers on their operator and allows an extended operator to wrap around the VcParD2 oligomer.

  • Organizational Affiliation

    Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antitoxin ParD
A, B, C, D, E
A, B, C, D, E, F, G, H
80Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: parDVC_A0360.1
Find proteins for P58093 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore P58093 
Go to UniProtKB:  P58093
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58093
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.08 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.272 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.01α = 90
b = 101.7β = 90
c = 107.23γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
MxCuBEdata collection
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description