Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.224 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Crystal structure of the site-specific recombinase, XerD.

Subramanya, H.S.Arciszewska, L.K.Baker, R.A.Bird, L.E.Sherratt, D.J.Wigley, D.B.

(1997) EMBO J 16: 5178-5187

  • DOI: https://doi.org/10.1093/emboj/16.17.5178
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The structure of the site-specific recombinase, XerD, that functions in circular chromosome separation, has been solved at 2.5 A resolution and reveals that the protein comprises two domains. The C-terminal domain contains two conserved sequence motifs that are located in similar positions in the structures of XerD, lambda and HP1 integrases. However, the extreme C-terminal regions of the three proteins, containing the active site tyrosine, are very different. In XerD, the arrangement of active site residues supports a cis cleavage mechanism. Biochemical evidence for DNA bending is encompassed in a model that accommodates extensive biochemical and genetic data, and in which the DNA is wrapped around an alpha-helix in a manner similar to that observed for CAP complexed with DNA.

  • Organizational Affiliation

    Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SITE-SPECIFIC RECOMBINASE XERD290Escherichia coliMutation(s): 0 
Find proteins for P0A8P8 (Escherichia coli (strain K12))
Explore P0A8P8 
Go to UniProtKB:  P0A8P8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8P8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.224 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.95α = 90
b = 102.95β = 90
c = 55.9γ = 120
Software Package:
Software NamePurpose
CCP4model building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-03-18
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Other