4QCA

Crystal structure of Vaccinia virus uracil-DNA glycosylase mutant R167AD4

• PDB DOI: https://doi.org/10.2210/pdb4QCA/pdb

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


• Deposited: 2014-05-09 Released: 2015-05-13 
• Deposition Author(s): Sartmatova, D., Nash, T., Schormann, N., Nuth, M., Ricciardi, R., Banerjee, S., Chattopadhyay, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Crystallization and preliminary X-ray diffraction analysis of three recombinant mutants of Vaccinia virus uracil DNA glycosylase.

Sartmatova, D., Nash, T., Schormann, N., Nuth, M., Ricciardi, R., Banerjee, S., Chattopadhyay, D.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 295-301

• PubMed: 23519808 
• DOI: https://doi.org/10.1107/S1744309113002716
• Primary Citation of Related Structures:  
  4QCA


• PubMed Abstract: 
  

  Amino-acid residues located at a highly flexible area in the uracil DNA glycosylase of Vaccinia virus were mutated. In the crystal structure of wild-type D4 these residues lie at the dimer interface. Specifically, three mutants were generated: (i) residue Arg167 was replaced with an alanine (R167AD4), (ii) residues Glu171, Ser172 and Pro173 were substituted with three glycine residues (3GD4) and (iii) residues Glu171 and Ser172 were deleted (Δ171-172D4). Mutant proteins were expressed, purified and crystallized in order to investigate the effects of these mutations on the structure of the protein.

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Organizational Affiliation: 

Science and Technology Honors Program, University of Alabama at Birmingham, Birmingham, AL 35294, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 101.66 kDa 
• Atom Count: 7,691 
• Modelled Residue Count: 881 
• Deposited Residue Count: 884 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uracil-DNA glycosylase	A, B, C, D	221	Vaccinia virus Ankara	Mutation(s): 2  Gene Names: ACAM3000_MVA_101, D4, MVA101R, UNG 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
GOL	E [auth A], I [auth C], K [auth D], L [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	G [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	F [auth A], H [auth B], J [auth C], M [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.14	α = 90
b = 118.268	β = 90
c = 121.97	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
RAPD	data collection
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-13 
Deposition Author(s): Sartmatova, D., Nash, T., Schormann, N., Nuth, M., Ricciardi, R., Banerjee, S., Chattopadhyay, D.

Revision History  

• Version 1.0: 2015-05-13
  Type: Initial release
  
• Version 1.1: 2016-06-29
  Changes: Source and taxonomy
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description