An activated, truncated gamma-delta resolvase tetramer

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Implications of structures of synaptic tetramers of gamma delta resolvase for the mechanism of recombination.

Kamtekar, S.Ho, R.S.Cocco, M.J.Li, W.Wenwieser, S.V.Boocock, M.R.Grindley, N.D.Steitz, T.A.

(2006) Proc Natl Acad Sci U S A 103: 10642-10647

  • DOI: https://doi.org/10.1073/pnas.0604062103
  • Primary Citation of Related Structures:  
    2GM4, 2GM5

  • PubMed Abstract: 

    The structures of two mutants of the site-specific recombinase, gammadelta resolvase, that form activated tetramers have been determined. One, at 3.5-A resolution, forms a synaptic intermediate of resolvase that is covalently linked to two cleaved DNAs, whereas the other is of an unliganded structure determined at 2.1-A resolution. Comparisons of the four known tetrameric resolvase structures show that the subunits interact through the formation of a common core of four helices. The N-terminal halves of these helices superimpose well on each other, whereas the orientations of their C termini are more variable. The catalytic domains of resolvase in the unliganded structure are arranged asymmetrically, demonstrating that their positions can move substantially while preserving the four-helix core that forms the tetramer. These results suggest that the precleavage synaptic tetramer of gammadelta resolvase, whose structure is not known, may be formed by a similar four-helix core, but differ in the relative orientations of its catalytic and DNA-binding domains.

  • Organizational Affiliation

    Departments of Molecular Biophysics, and Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transposon gamma-delta resolvase
A, B, C, D
139Escherichia coliMutation(s): 9 
Gene Names: tnpR
Find proteins for P03012 (Escherichia coli (strain K12))
Explore P03012 
Go to UniProtKB:  P03012
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03012
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B, C, D
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.331α = 90
b = 98.476β = 90
c = 100.408γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations