4DOF | pdb_00004dof

Structures of Vaccinia Virus Uracil-DNA Glycosylase in New Crystal Forms

PDB DOI: https://doi.org/10.2210/pdb4DOF/pdb

Classification: HYDROLASE
Organism(s): Vaccinia virus Western Reserve
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-02-09 Released: 2013-02-20
Deposition Author(s): Schormann, N., Chattopadhyay, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.269 (Depositor), 0.268 (DCC)
R-Value Work:
0.221 (Depositor), 0.220 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Analysis of the Dimer Interface in Crystal Structures of Vaccinia Virus Uracil DNA Glycosylase

Schormann, N., Sommers, C.I., Ricciardi, R.P., Chattopadhyay, D.

To be published.

Macromolecule Content

Total Structure Weight: 109.01 kDa
Atom Count: 7,159
Modeled Residue Count: 872
Deposited Residue Count: 952
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uracil-DNA glycosylase	A, B, C, D	238	Vaccinia virus Western Reserve	Mutation(s): 1 Gene Names: D4R, VACWR109 EC: 3.2.2.27
UniProt
Find proteins for P04303 (Vaccinia virus (strain Western Reserve)) Explore P04303 Go to UniProtKB: P04303
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04303
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.269 (Depositor), 0.268 (DCC)
R-Value Work: 0.221 (Depositor), 0.220 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.2	α = 90
b = 102.88	β = 90
c = 117.24	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-02-20

Deposition Author(s):

Chattopadhyay, D.

Revision History (Full details and data files)

Version 1.0: 2013-02-20
Type: Initial release
Version 1.1: 2016-06-29
Changes: Source and taxonomy
Version 1.2: 2023-09-13
Changes: Data collection, Database references, 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.