2FPK

RadA recombinase in complex with ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.234 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Crystal Structure of Methanococcus Voltae Rada in Complex with Adp: hydrolysis-induced conformational change

Qian, X.Wu, Y.He, Y.Moya, I.A.Luo, Y.

(2005) Biochemistry 44: 13753-13761

  • DOI: https://doi.org/10.1021/bi051222i
  • Primary Citation of Related Structures:  
    2FPK, 2FPL, 2FPM

  • PubMed Abstract: 

    Members of a superfamily of RecA-like recombinases facilitate a central strand exchange reaction in the DNA repair process. Archaeal RadA and Rad51 and eukaryal Rad51 and meiosis-specific DMC1 form a closely related group of recombinases distinct from bacterial RecA. Nevertheless, all such recombinases share a conserved core domain which carries the ATPase site and putative DNA-binding sites. Here we present the crystal structure of an archaeal RadA from Methanococcus voltae (MvRadA) in complex with ADP and Mg2+ at 2.1 A resolution. The crystallized RadA-ADP filament has an extended helical pitch similar to those of previously determined structures in the presence of nonhydrolyzable ATP analogue AMP-PNP. Structural comparison reveals two recurrent conformations with an extensive allosteric effect spanning the ATPase site and the putative DNA-binding L2 region. Varied conformations of the L2 region also imply a dynamic nature of recombinase-bound DNA.


  • Organizational Affiliation

    Department of Biochemistry, University of Saskatchewan, A3 Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan, Canada S7N 5E5.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair and recombination protein radA322Methanococcus voltaeMutation(s): 1 
Gene Names: RADA
UniProt
Find proteins for O73948 (Methanococcus voltae)
Explore O73948 
Go to UniProtKB:  O73948
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO73948
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.234 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.986α = 90
b = 83.986β = 90
c = 106.367γ = 120
Software Package:
Software NamePurpose
SAINTPLUSdata collection
LSCALEdata reduction
AMoREphasing
CNSrefinement
SAINTdata reduction
LSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-31
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-30
    Changes: Data collection, Refinement description