1GDT

CRYSTAL STRUCTURE OF A SITE-SPECIFIC RECOMBINASE, GAMMA-DELTA RESOLVASE COMPLEXED WITH A 34 BP CLEAVAGE SITE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of the site-specific recombinase gamma delta resolvase complexed with a 34 bp cleavage site.

Yang, W., Steitz, T.A.

(1995) Cell 82: 193-207

  • DOI: 10.1016/0092-8674(95)90307-0
  • Primary Citation of Related Structures:  
    1GDT

  • PubMed Abstract: 

    • The structure of gamma delta resolvase complexed with a 34 bp substrate DNA has been determined at 3.0 A resolution. The DNA is sharply bent by 60 degrees toward the major groove and away from the resolvase catalytic domains at the recombination crossover point ...

    The structure of gamma delta resolvase complexed with a 34 bp substrate DNA has been determined at 3.0 A resolution. The DNA is sharply bent by 60 degrees toward the major groove and away from the resolvase catalytic domains at the recombination crossover point. The C-terminal one third of resolvase, which was disordered in the absence of DNA, forms an arm and a 3-helix DNA-binding domain on the opposite side of the DNA from the N-terminal domain. The arms wrap around the minor groove of the central 16 bp, and the DNA-binding domains interact with the major grooves near the outer boundaries of the binding site. The resolvase dimer is asymmetric, particularly in the arm region, implying a conformational adaptability that may be important for resolvase binding to different DNA sites in the synaptosome. It also raises the possibility of a sequential single-strand cleavage mechanism.

    Organizational Affiliation: 

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (GAMMA DELTA RESOLVASE)E [auth A], F [auth B]183Escherichia coliMutation(s): 0 
Gene Names: tnpR
Find proteins for P03012 (Escherichia coli (strain K12))
Explore P03012 
Go to UniProtKB:  P03012
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
SITE I OF RES DNAA [auth C]22N/A
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    SITE I OF RES DNAB [auth D], D [auth F]13N/A
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    (by identity cutoff)  |  Structure
    Entity ID: 3
    MoleculeChainsLengthOrganismImage
    SITE I OF RES DNAC [auth E]21N/A
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.00 Å
    • R-Value Work: 0.235 
    • R-Value Observed: 0.235 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 113α = 90
    b = 157β = 90
    c = 37.2γ = 90
    Software Package:
    Software NamePurpose
    X-PLORrefinement
    DENZOdata reduction
    SCALEPACKdata scaling

    Structure Validation

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    Entry History 

    Deposition Data

    • Deposited Date: 1995-04-11 
    • Released Date: 1996-04-03 
      • Deposition Author(s): Yang, W., Steitz, T.A.

    Revision History  (Full details and data files)

    • Version 1.0: 1996-04-03
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance