6YJB

VcaM4I restriction endonuclease 5hmC-ssDNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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 endonucleaseA309Vibrio 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*AP*(5HC)P*AP*G)-3')B5synthetic construct
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SO4
    Query on SO4

    Download Ideal Coordinates CCD File 
    A, B
    SULFATE ION
    O4 S
    QAOWNCQODCNURD-UHFFFAOYSA-L
     Ligand Interaction
    GOL
    Query on GOL

    Download Ideal Coordinates CCD File 
    A, B
    GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N
     Ligand Interaction
    CL
    Query on CL

    Download Ideal Coordinates CCD File 
    A
    CHLORIDE ION
    Cl
    VEXZGXHMUGYJMC-UHFFFAOYSA-M
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.55 Å
    • R-Value Free: 0.164 
    • R-Value Work: 0.142 
    • R-Value Observed: 0.144 
    • Space Group: P 62 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 128.685α = 90
    b = 128.685β = 90
    c = 110.895γ = 120
    Software Package:
    Software NamePurpose
    REFMACrefinement
    XDSdata reduction
    XDSdata scaling
    PHASERphasing
    PDB_EXTRACTdata extraction

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2020-12-23
      Type: Initial release
    • Version 1.1: 2020-12-30
      Changes: Experimental preparation