1GDR

MODEL FOR A DNA MEDIATED SYNAPTIC COMPLEX SUGGESTED BY CRYSTAL PACKING OF GAMMA DELTA RESOLVASE SUBUNITS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Work: 0.310 
  • R-Value Observed: 0.310 

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This is version 1.3 of the entry. See complete history


Literature

Model for a DNA-mediated synaptic complex suggested by crystal packing of gamma delta resolvase subunits.

Rice, P.A.Steitz, T.A.

(1994) EMBO J 13: 1514-1524

  • DOI: https://doi.org/10.2210/pdb1gdr/pdb
  • Primary Citation of Related Structures:  
    1GDR

  • PubMed Abstract: 

    The packing arrangement of the 12 subunits of intact gamma delta resolvase in the unit cell of a hexagonal crystal form suggests a model for site-specific recombination that involves a DNA-mediated synaptic intermediate. The crystal structure has been determined by molecular replacement and partially refined at 2.8/3.5 A resolution. Although the small DNA-binding domain is disordered in these crystals, packing considerations show that only a small region of space in the crystal could accommodate a domain of its size. A family of related models for a synaptic complex between two DNA duplexes and 12 monomers that are arranged as situated in the crystal is consistent with the known topology of the complex and the distances between the three resolvase dimer-binding sites per DNA; further, these models place the two DNA recombination sites in contact with each other between two resolvase dimers, implying that strand exchange is accomplished through direct DNA-DNA interaction. A major role postulated, then, for the resolvase protein assembly is to stabilize a res DNA structure that is close to the topological transition state of the reaction.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, CT.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GAMMA DELTA-RESOLVASE140Escherichia coliMutation(s): 0 
UniProt
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Work: 0.310 
  • R-Value Observed: 0.310 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.2α = 90
b = 60.2β = 90
c = 170.1γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-04-30
    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, Derived calculations, Other