Crystal Structure of mycobacteriophage Pukovnik Xis

Experimental Data Snapshot

  • Resolution: 2.35 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

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The Structure of Xis Reveals the Basis for Filament Formation and Insight into DNA Bending within a Mycobacteriophage Intasome.

Singh, S.Plaks, J.G.Homa, N.J.Amrich, C.G.Heroux, A.Hatfull, G.F.Vandemark, A.P.

(2014) J Mol Biol 426: 412-422

  • DOI: https://doi.org/10.1016/j.jmb.2013.10.002
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The recombination directionality factor, Xis, is a DNA bending protein that determines the outcome of integrase-mediated site-specific recombination by redesign of higher-order protein-DNA architectures. Although the attachment site DNA of mycobacteriophage Pukovnik is likely to contain four sites for Xis binding, Xis crystals contain five subunits in the asymmetric unit, four of which align into a Xis filament and a fifth that is generated by an unusual domain swap. Extensive intersubunit contacts stabilize a bent filament-like arrangement with Xis monomers aligned head to tail. The structure implies a DNA bend of ~120°, which is in agreement with DNA bending measured in vitro. Formation of attR-containing intasomes requires only Int and Xis, distinguishing Pukovnik from lambda. Therefore, we conclude that, in Pukovnik, Xis-induced DNA bending is sufficient to promote intramolecular Int-mediated bridges during intasome formation.

  • Organizational Affiliation

    Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C [auth D],
D [auth C],
58Pukovnikvirus pukovnikMutation(s): 0 
Gene Names: 37Pukovnik_37XIS
Find proteins for B3VGI6 (Pukovnikvirus pukovnik)
Explore B3VGI6 
Go to UniProtKB:  B3VGI6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3VGI6
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.35 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.423α = 90
b = 129.985β = 90
c = 92.346γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations