2W8M | pdb_00002w8m

Structure of D212, a nuclease from a fusselovirus.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.245 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

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This is version 1.3 of the entry. See complete history. 


Literature

The crystal structure of D212 from sulfolobus spindle-shaped virus ragged hills reveals a new member of the PD-(D/E)XK nuclease superfamily.

Menon, S.K., Eilers, B.J., Young, M.J., Lawrence, C.M.

(2010) J Virol 84: 5890-5897

  • DOI: https://doi.org/10.1128/JVI.01663-09
  • Primary Citation of Related Structures:  
    2W8M

  • PubMed Abstract: 

    Structural studies have made significant contributions to our understanding of Sulfolobus spindle-shaped viruses (Fuselloviridae), an important model system for archaeal viruses. Continuing these efforts, we report the structure of D212 from Sulfolobus spindle-shaped virus Ragged Hills. The overall fold and conservation of active site residues place D212 in the PD-(D/E)XK nuclease superfamily. The greatest structural similarity is found to the archaeal Holliday junction cleavage enzymes, strongly suggesting a role in DNA replication, repair, or recombination. Other roles associated with nuclease activity are also considered.

    • Organizational Affiliation: 

    Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ORF D212
A, B
212Sulfolobus virus Ragged HillsMutation(s): 0 
UniProt
Find proteins for Q6TRV5 (Sulfolobus virus Ragged Hills)
Explore Q6TRV5 
Go to UniProtKB:  Q6TRV5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6TRV5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.245 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.477α = 90
b = 81.971β = 115.4
c = 60.16γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2018-06-13
    Changes: Advisory, Data collection, Database references
  • Version 1.3: 2024-05-08
    Changes: Advisory, Data collection, Database references, Other