2OFO

MSrecA-native


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1016/j.jmb.2007.01.058
  • Primary Citation of Related Structures:  

  • 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 t ...

    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.


    Related Citations: 
    • Crystal structures of Mycobacterium tuberculosis RecA and its complex with ADP-AlF(4): implications for decreased ATPase activity and molecular aggregation
      Datta, S.,Prabu, M.M.,Vaze, M.B.,Ganesh, N.,Chandra, N.R.,Muniyappa, K.,Vijayan, M.
      (2000) Nucleic Acids Res. 28: 4964
    • Crystallographic identification of an ordered C-terminal domain and a second nucleotide-binding site in RecA: new insights into allostery
      Krishna, R.,Manjunath, G.P.,Kumar, P.,Surolia, A.,Chandra, N.R.,Muniyappa, K.,Vijayan, M.
      (2006) Nucleic Acids Res. 34: 2186
    • Structural studies on MtRecA-nucleotide complexes: insights into DNA and nucleotide binding and the structural signature of NTP recognition
      Datta, S.,Ganesh, N.,Chandra, N.R.,Muniyappa, K.,Vijayan, M.
      (2003) Proteins 50: 474
    • Crystal structures of Mycobacterium smegmatis RecA and its nucleotide complexes
      Datta, S.,Krishna, R.,Ganesh, N.,Chandra, N.R.,Muniyappa, K.,Vijayan, M.
      (2003) J.Bacteriol. 185: 4280


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein recA
A
349Mycobacterium smegmatisMutation(s): 0 
Gene Names: recA
Find proteins for Q5QJ16 (Mycobacterium smegmatis)
Go to UniProtKB:  Q5QJ16
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.216 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 108.418α = 90.00
b = 108.418β = 90.00
c = 72.173γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance