3JSC

CcdBVfi-FormI-pH7.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and thermodynamic characterization of vibrio fischeri CCDB

De Jonge, N.Hohlweg, W.Garcia-Pino, A.Respondek, M.Buts, L.Haesaerts, S.Lah, J.Zangger, K.Loris, R.

(2010) J.Biol.Chem. 285: 5606-5613

  • DOI: 10.1074/jbc.M109.068429
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CcdB(Vfi) from Vibrio fischeri is a member of the CcdB family of toxins that poison covalent gyrase-DNA complexes. In solution CcdB(Vfi) is a dimer that unfolds to the corresponding monomeric components in a two-state fashion. In the unfolded state, ...

    CcdB(Vfi) from Vibrio fischeri is a member of the CcdB family of toxins that poison covalent gyrase-DNA complexes. In solution CcdB(Vfi) is a dimer that unfolds to the corresponding monomeric components in a two-state fashion. In the unfolded state, the monomer retains a partial secondary structure. This observation correlates well with the crystal and NMR structures of the protein, which show a dimer with a hydrophobic core crossing the dimer interface. In contrast to its F plasmid homologue, CcdB(Vfi) possesses a rigid dimer interface, and the apparent relative rotations of the two subunits are due to structural plasticity of the monomer. CcdB(Vfi) shows a number of non-conservative substitutions compared with the F plasmid protein in both the CcdA and the gyrase binding sites. Although variation in the CcdA interaction site likely determines toxin-antitoxin specificity, substitutions in the gyrase-interacting region may have more profound functional implications.


    Related Citations: 
    • Purification and crystallization of Vibrio fischeri CcdB and its complexes with fragments of gyrase and CcdA
      De Jonge, N.,Buts, L.,Vangelooven, J.,Mine, N.,Van Melderen, L.,Wyns, L.,Loris, R.
      (2007) Acta Crystallogr.,Sect.F 63: 356


    Organizational Affiliation

    Structural Biology Brussels, and Department of Molecular and Cellular Interactions, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CcdB
A
105Aliivibrio fischeriMutation(s): 0 
Gene Names: ccdB
Find proteins for Q84B82 (Aliivibrio fischeri)
Go to UniProtKB:  Q84B82
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.172 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 84.487α = 90.00
b = 84.487β = 90.00
c = 84.487γ = 90.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
DENZOdata reduction
PHASERphasing
PHENIXrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance