6WE1

Wheat dwarf virus Rep domain complexed with a single-stranded DNA 8-mer comprising the cleavage site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report



Literature

Wheat dwarf virus Rep domain complexed with a single-stranded DNA 8-mer comprising the cleavage site

Tompkins, K.

To be published.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Replication-associated proteinAD139Wheat dwarf virusMutation(s): 1 
Gene Names: rep
EC: 3.1.21
Find proteins for A0A0F6N3D1 (Wheat dwarf virus)
Explore A0A0F6N3D1 
Go to UniProtKB:  A0A0F6N3D1
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*AP*TP*AP*TP*TP*AP*C)-3')C, F8Wheat dwarf virus
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MN
    Query on MN

    Download Ideal Coordinates CCD File 
    A, C, D
    MANGANESE (II) ION
    Mn
    WAEMQWOKJMHJLA-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.61 Å
    • R-Value Free: 0.243 
    • R-Value Work: 0.188 
    • R-Value Observed: 0.191 
    • Space Group: P 41 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 50.626α = 90
    b = 50.626β = 90
    c = 241.977γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    PDB_EXTRACTdata extraction
    HKL-2000data reduction
    HKL-2000data scaling
    PHENIXphasing
    Cootmodel building

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM119483

    Revision History 

    • Version 1.0: 2020-12-16
      Type: Initial release