4DOG | pdb_00004dog

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

• PDB DOI: https://doi.org/10.2210/pdb4DOG/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 25.52 kDa 
• Atom Count: 1,774 
• Modeled Residue Count: 215 
• Deposited Residue Count: 221 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uracil-DNA glycosylase	A	221	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.79	α = 90
b = 85.79	β = 90
c = 123.46	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-20 
Deposition Author(s): Schormann, N., Chattopadhyay, D.

Revision History  

• 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, Derived calculations, Refinement description