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 Å
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


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


  • 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 cros ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (GAMMA DELTA RESOLVASE)
A, B
183Escherichia coli (strain K12)Gene Names: tnpR
Find proteins for P03012 (Escherichia coli (strain K12))
Go to UniProtKB:  P03012
Entity ID: 1
MoleculeChainsLengthOrganism
SITE I OF RES DNAC22N/A
Entity ID: 2
MoleculeChainsLengthOrganism
SITE I OF RES DNAD,F13N/A
Entity ID: 3
MoleculeChainsLengthOrganism
SITE I OF RES DNAE21N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Work: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 113.000α = 90.00
b = 157.000β = 90.00
c = 37.200γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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