5C6K | pdb_00005c6k

Bacteriophage P2 integrase catalytic domain

• PDB DOI: https://doi.org/10.2210/pdb5C6K/pdb

• Classification: HYDROLASE
• Organism(s): Peduovirus P2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-06-23 Released: 2015-10-21 
• Deposition Author(s): Skaar, K., Claesson, M., Odegrip, R., Eriksson, J., Hogbom, M., Haggard-Ljungquist, E., Stenmark, P.
• Funding Organization(s): Swedish Research Council, Carl Tryggers Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.201 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the bacteriophage P2 integrase catalytic domain.

Skaar, K., Claesson, M., Odegrip, R., Hogbom, M., Haggard-Ljungquist, E., Stenmark, P.

(2015) FEBS Lett 589: 3556-3563

• PubMed: 26453836 
• DOI: https://doi.org/10.1016/j.febslet.2015.09.026
• Primary Citation Related Structures: 
  5C6K, 5DOR


• PubMed Abstract: 
  

  Bacteriophage P2 is a temperate phage capable of integrating its DNA into the host genome by site-specific recombination upon lysogenization. Integration and excision of the phage genome requires P2 integrase, which performs recognition, cleavage and joining of DNA during these processes. This work presents the high-resolution crystal structure of the catalytic domain of P2 integrase, and analysis of the structure-function relationship of several previously identified non-functional P2 integrase mutants. The DNA binding area is characterized by a large positively charged patch, harboring key residues. The structure reveals potential for large dimer flexibility, likely essential for rearrangement of DNA strands upon integration and excision of the phage DNA.

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Organizational Affiliation: 
• Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.05 kDa 
• Atom Count: 2,879 
• Modeled Residue Count: 332 
• Deposited Residue Count: 584 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A, B	292	Peduovirus P2	Mutation(s): 0  Gene Names: int EC: 3.1 (UniProt), 2.7.7 (UniProt)
UniProt
Find proteins for P36932 (Escherichia phage P2) Explore P36932  Go to UniProtKB:  P36932

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.201 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 215.004	α = 90
b = 54.42	β = 97.33
c = 38.61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-10-21 
Deposition Author(s): Skaar, K., Claesson, M., Odegrip, R., Eriksson, J., Hogbom, M., Haggard-Ljungquist, E., Stenmark, P.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2010-5200
Swedish Research Council	Sweden	2014-5667
Carl Tryggers Foundation	Sweden	--

Revision History  

• Version 1.0: 2015-10-21
  Type: Initial release
  
• Version 1.1: 2015-12-02
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description