3BVP | pdb_00003bvp

Crystal Structure of the N-terminal Catalytic Domain of TP901-1 Integrase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.263 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Tetrameric structure of a serine integrase catalytic domain.

Yuan, P.Gupta, K.Van Duyne, G.D.

(2008) Structure 16: 1275-1286

  • DOI: https://doi.org/10.1016/j.str.2008.04.018
  • Primary Citation Related Structures: 
    3BVP

  • PubMed Abstract: 

    The serine integrases have recently emerged as powerful new chromosome engineering tools in various organisms and show promise for therapeutic use in human cells. The serine integrases are structurally and mechanistically unrelated to the bacteriophage lambda integrase but share a similar catalytic domain with the resolvase/invertase enzymes typified by the resolvase proteins from transposons Tn3 and gammadelta. Here we report the crystal structure and solution properties of the catalytic domain from bacteriophage TP901-1 integrase. The protein is a dimer in solution but crystallizes as a tetramer that is closely related in overall architecture to structures of activated gammadelta-resolvase mutants. The ability of the integrase tetramer to explain biochemical experiments performed in the resolvase and invertase systems suggests that the TP901 integrase tetramer represents a unique intermediate on the recombination pathway that is shared within the serine recombinase superfamily.


  • Organizational Affiliation
    • Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.

Macromolecule Content 

  • Total Structure Weight: 31.52 kDa 
  • Atom Count: 2,348 
  • Modeled Residue Count: 266 
  • Deposited Residue Count: 276 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TP901-1 Integrase
A, B
138Lactococcus phage TP901-1Mutation(s): 0 
Gene Names: int
UniProt
Find proteins for Q38184 (Lactococcus phage TP901-1)
Explore Q38184 
Go to UniProtKB:  Q38184
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ38184
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.263 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.229α = 90
b = 67.229β = 90
c = 174.565γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2012-03-21
    Changes: Database references
  • Version 1.3: 2017-10-25
    Changes: Refinement description
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references