Experimental Data Snapshot

  • Resolution: 3.16 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 

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Snapshots of RecA protein involving movement of the C-domain and different conformations of the DNA-binding loops: crystallographic and comparative analysis of 11 structures of Mycobacterium smegmatis RecA

Krishna, R.Prabu, J.R.Manjunath, G.P.Datta, S.Chandra, N.R.Muniyappa, K.Vijayan, M.

(2007) J Mol Biol 367: 1130-1144

  • DOI: https://doi.org/10.1016/j.jmb.2007.01.058
  • Primary Citation of Related Structures:  
    2ODN, 2ODW, 2OE2, 2OEP, 2OES, 2OFO

  • PubMed Abstract: 

    Mycobacterium smegmatis RecA and its nucleotide complexes crystallize in three different, but closely related, forms characterized by specific ranges of unit cell dimensions. The six crystals reported here and five reported earlier, all grown under the same or very similar conditions, belong to these three forms, all in space group P6(1). They include one obtained by reducing relative humidity around the crystal. In all crystals, RecA monomers form filaments around a 6(1) screw axis. Thus, the c-dimension of the crystal corresponds to the pitch of the RecA filament. As reported for Escherichia coli RecA, the variation in the pitch among the three forms correlates well with the motion of the C-terminal domain of the RecA monomers with respect to the main domain. The domain motion is compatible with formation of inactive as well as active RecA filaments involving monomers with a fully ordered C domain. It does not appear to influence the movement upon nucleotide-binding of the switch residue, which is believed to provide the trigger for transmitting the effect of nucleotide binding to the DNA-binding region. Interestingly, partial dehydration of the crystal results in the movement of the residue similar to that caused by nucleotide binding. The ordering of the DNA-binding loops, which present ensembles of conformations, is also unaffected by domain motion. The conformation of loop L2 appears to depend upon nucleotide binding, presumably on account of the movement of the switch residue that forms part of the loop. The conformations of loops L1 and L2 are correlated and have implications for intermolecular communications within the RecA filament. The structures resulting from different orientations of the C domain and different conformations of the DNA-binding loops appear to represent snapshots of the RecA at different phases of activity, and provide insights into the mechanism of action of RecA.

  • Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560 012, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein recA349Mycolicibacterium smegmatisMutation(s): 0 
Find proteins for Q5QJ16 (Mycolicibacterium smegmatis)
Explore Q5QJ16 
Go to UniProtKB:  Q5QJ16
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5QJ16
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PO4

Download Ideal Coordinates CCD File 
O4 P
Experimental Data & Validation

Experimental Data

  • Resolution: 3.16 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.418α = 90
b = 108.418β = 90
c = 72.173γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-19
    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: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description