4IRB | pdb_00004irb

Crystal Structure of Vaccinia Virus Uracil DNA Glycosylase Mutant del171-172D4

• PDB DOI: https://doi.org/10.2210/pdb4IRB/pdb

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


• Deposited: 2013-01-14 Released: 2014-02-26 
• Deposition Author(s): Schormann, N., Zhukovskaya, N., Sartmatova, D., Nuth, M., Ricciardi, R.P., Chattopadhyay, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.258 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.211 (Depositor) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Mutations at the dimer interface affect both function and structure of the Vaccinia virus uracil DNA glycosylase

Schormann, N., Zhukovskaya, N., Sartmatova, D., Nuth, M., 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 108.66 kDa 
• Atom Count: 7,087 
• Modeled Residue Count: 862 
• Deposited Residue Count: 944 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uracil-DNA glycosylase	A, B, C, D	236	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], G [auth B], I [auth C], J [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.258 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.211 (Depositor) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.9	α = 90
b = 130.51	β = 90
c = 86.31	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-26 
Deposition Author(s): Schormann, N., Zhukovskaya, N., Sartmatova, D., Nuth, M., Ricciardi, R.P., Chattopadhyay, D.

Revision History  

• Version 1.0: 2014-02-26
  Type: Initial release
  
• Version 1.1: 2016-06-29
  Changes: Structure summary
• Version 1.2: 2017-11-22
  Changes: Database references
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary