6YMG

VcaM4I restriction endonuclease in complex with 5mC-modified dsDNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report



Literature

Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA

Pastor, M.Czapinska, H.Lutz, T.Helbrecht, I.Xu, S.Bochtler, M.

(2020) Nucleic Acids Res 


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HNH endonucleaseAB309Vibrio campbelliiMutation(s): 0 
Gene Names: DSB67_20905
Find proteins for A0A344KQF3 (Vibrio campbellii)
Explore A0A344KQF3 
Go to UniProtKB:  A0A344KQF3
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*A)-3')C, E11synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3')D, F11synthetic construct
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.14 Å
      • R-Value Free: 0.266 
      • R-Value Work: 0.241 
      • R-Value Observed: 0.243 
      • Space Group: P 61 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 81.111α = 90
      b = 81.111β = 90
      c = 617.307γ = 120
      Software Package:
      Software NamePurpose
      REFMACrefinement
      PDB_EXTRACTdata extraction
      XDSdata reduction
      XDSdata scaling
      PHASERphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2020-12-23
        Type: Initial release