2OXO

Crystallization and structure determination of the core-binding domain of bacteriophage lambda integrase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystallization and structure determination of the core-binding domain of bacteriophage lambda integrase.

Kamadurai, H.B.Jain, R.Foster, M.P.

(2008) Acta Crystallogr.,Sect.F 64: 470-473

  • DOI: 10.1107/S174430910801381X

  • PubMed Abstract: 
  • Bacteriophage lambda integrase catalyzes site-specific DNA recombination. A helical bundle domain in the enzyme, called the core-binding domain (Int(CB)), promotes the catalysis of an intermediate DNA-cleavage reaction that is critical for recombinat ...

    Bacteriophage lambda integrase catalyzes site-specific DNA recombination. A helical bundle domain in the enzyme, called the core-binding domain (Int(CB)), promotes the catalysis of an intermediate DNA-cleavage reaction that is critical for recombination and is not well folded in solution in the absence of DNA. To gain structural insights into the mechanism behind the accessory role of this domain in catalysis, an attempt was made to crystallize an Int(CB)-DNA complex, but crystals of free Int(CB) were fortuitously obtained. The three-dimensional structure of DNA-free Int(CB) was solved at 2.0 A resolution by molecular replacement using as the search model the previously available DNA-bound 2.8 A structure of the Int(CB) domain in a larger construct of lambda integrase. The crystal structure of DNA-free Int(CB) resembles the DNA-bound structure of Int(CB), but exhibits subtle differences in the DNA-binding face and lacks electron density for ten residues in the C-terminus that form a portion of a linker connecting Int(CB) to the C-terminal catalytic domain of the enzyme. Thus, this work reveals the domain in the absence of DNA and allows comparison with the DNA-bound form of this catalytically activating domain.


    Organizational Affiliation

    Biophysics Program and Department of Biochemistry, The Ohio State University, Columbus, OH 43201, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrase
A
103Escherichia phage lambdaMutation(s): 0 
Gene Names: int
EC: 2.7.7.-, 3.1.-.-
Find proteins for P03700 (Escherichia phage lambda)
Go to UniProtKB:  P03700
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.228 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 46.693α = 90.00
b = 46.693β = 90.00
c = 111.533γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
CrystalCleardata collection
d*TREKdata scaling
CrystalCleardata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance