2W8M | pdb_00002w8m

Structure of D212, a nuclease from a fusselovirus.

PDB DOI: https://doi.org/10.2210/pdb2W8M/pdb

Classification: HYDROLASE
Organism(s): Sulfolobus virus Ragged Hills
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-01-17 Released: 2009-02-03
Deposition Author(s): Menon, S.K., Young, M.J., Lawrence, C.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.245 (Depositor), 0.263 (DCC)
R-Value Work:
0.209 (Depositor), 0.215 (DCC)
R-Value Observed:
0.211 (Depositor)

wwPDB Validation 3D Report Full Report

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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

PubMed: 20375162 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1128/JVI.01663-09
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 50.21 kDa
Atom Count: 2,892
Modeled Residue Count: 333
Deposited Residue Count: 424
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF D212	A, B	212	Sulfolobus virus Ragged Hills	Mutation(s): 0
UniProt
Find proteins for Q6TRV5 (Sulfolobus virus Ragged Hills) Explore Q6TRV5 Go to UniProtKB: Q6TRV5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6TRV5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.245 (Depositor), 0.263 (DCC)
R-Value Work: 0.209 (Depositor), 0.215 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.477	α = 90
b = 81.971	β = 115.4
c = 60.16	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-02-03

Deposition Author(s):

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.