1A0P | pdb_00001a0p

SITE-SPECIFIC RECOMBINASE, XERD

• PDB DOI: https://doi.org/10.2210/pdb1A0P/pdb

• Classification: DNA RECOMBINATION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-12-05 Released: 1998-03-18 
• Deposition Author(s): Subramanya, H.S., Arciszewska, L.K., Baker, R.A., Bird, L.E., Sherratt, D.J., Wigley, D.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.287 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.210 (DCC) 

Literature

Crystal structure of the site-specific recombinase, XerD.

Subramanya, H.S., Arciszewska, L.K., Baker, R.A., Bird, L.E., Sherratt, D.J., Wigley, D.B.

(1997) EMBO J 16: 5178-5187

• PubMed: 9311978 
• DOI: https://doi.org/10.1093/emboj/16.17.5178
• Primary Citation Related Structures: 
  1A0P


• PubMed Abstract: 
  

  The structure of the site-specific recombinase, XerD, that functions in circular chromosome separation, has been solved at 2.5 A resolution and reveals that the protein comprises two domains. The C-terminal domain contains two conserved sequence motifs that are located in similar positions in the structures of XerD, lambda and HP1 integrases. However, the extreme C-terminal regions of the three proteins, containing the active site tyrosine, are very different. In XerD, the arrangement of active site residues supports a cis cleavage mechanism. Biochemical evidence for DNA bending is encompassed in a model that accommodates extensive biochemical and genetic data, and in which the DNA is wrapped around an alpha-helix in a manner similar to that observed for CAP complexed with DNA.

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Organizational Affiliation: 
• Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.31 kDa 
• Atom Count: 2,310 
• Modeled Residue Count: 271 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SITE-SPECIFIC RECOMBINASE XERD	A	290	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A8P8 (Escherichia coli (strain K12)) Explore P0A8P8  Go to UniProtKB:  P0A8P8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.287 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.210 (DCC) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.95	α = 90
b = 102.95	β = 90
c = 55.9	γ = 120

Software Package:

Software Name	Purpose
CCP4	model building
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-03-18 
Deposition Author(s): Subramanya, H.S., Arciszewska, L.K., Baker, R.A., Bird, L.E., Sherratt, D.J., Wigley, D.B.

Revision History  

• Version 1.0: 1998-03-18
  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, Other