2V6J | pdb_00002v6j

Kokobera Virus Helicase: Mutant Met47Thr

PDB DOI: https://doi.org/10.2210/pdb2V6J/pdb

Classification: HYDROLASE
Organism(s): Kokobera virus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2007-07-18 Released: 2008-03-25
Deposition Author(s): Speroni, S., De Colibus, L., Coutard, B., Canard, B., Mattevi, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.258 (Depositor), 0.268 (DCC)
R-Value Work:
0.223 (Depositor)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Structure and Biochemical Analysis of Kokobera Virus Helicase

Speroni, S., De Colibus, L., Mastrangelo, E., Gould, E., Coutard, B., Forrester, N.L., Blanc, S., Canard, B., Mattevi, A.

(2008) Proteins 70: 1120

PubMed: 18004778 Search on PubMed
DOI: https://doi.org/10.1002/prot.21812
Primary Citation Related Structures:
2V6I, 2V6J

Organizational Affiliation

Department of Genetics and Microbiology, University of Pavia, via Ferrata 1, Pavia 27100 Italy.

Macromolecule Content

Total Structure Weight: 48.97 kDa
Atom Count: 3,462
Modeled Residue Count: 421
Deposited Residue Count: 431
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA HELICASE	A	431	Kokobera virus	Mutation(s): 1
UniProt
Find proteins for Q32ZD5 (Kokobera virus) Explore Q32ZD5 Go to UniProtKB: Q32ZD5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q32ZD5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.258 (Depositor), 0.268 (DCC)
R-Value Work: 0.223 (Depositor)
R-Value Observed: 0.224 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.57	α = 90
b = 88.57	β = 90
c = 138.579	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-03-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-03-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2018-01-24
Changes: Source and taxonomy
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description

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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.