4WRK | pdb_00004wrk

The 3D structure of D95N mutant DUTPase from phage phi11 of S. aureus reveals the molecular details for the coordination of a structural Mg(II) ion

• PDB DOI: https://doi.org/10.2210/pdb4WRK/pdb

• Classification: HYDROLASE
• Organism(s): Dubowvirus dv11
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-10-24 Released: 2015-12-23 
• Deposition Author(s): Bendes, A.A., Leveles, I., Vertessy, B.G.
• Funding Organization(s): ungarian Scientific Research Fund OTKA, Baross Program of the New Hungary Development Plan, Hungarian Academy of Sciences, European Union

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.258 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

The 3D structure of D95N mutant DUTPase from phage phi11 of S. aureus reveals the molecular details for the coordination of a structural Mg(II) ion

Bendes, A.A., Leveles, I., Vertessy, B.G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 113.27 kDa 
• Atom Count: 7,158 
• Modeled Residue Count: 927 
• Deposited Residue Count: 1,014 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUTPase	A, B, C, D, E, F	169	Dubowvirus dv11	Mutation(s): 1  EC: 3.6.1.23
UniProt
Find proteins for Q8SDV3 (Staphylococcus phage phi11) Explore Q8SDV3  Go to UniProtKB:  Q8SDV3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DUP	G [auth A], I [auth B], K [auth C], M [auth D], N [auth D], Q [auth F]	2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE C9 H16 N3 O13 P3 XZLLMTSKYYYJLH-SHYZEUOFSA-N
MG	H [auth A], J [auth B], L [auth C], O [auth D], P [auth E], R [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.258 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.42	α = 90
b = 108.42	β = 90
c = 167.05	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-12-23 
Deposition Author(s): Bendes, A.A., Leveles, I., Vertessy, B.G.

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Funding Organization	Location	Grant Number
ungarian Scientific Research Fund OTKA	Hungary	NK 84008
ungarian Scientific Research Fund OTKA	Hungary	K109486
Baross Program of the New Hungary Development Plan	Hungary	3DSTRUCT, MFB-00266/2010 REG-KM-09-1-2009-005
Hungarian Academy of Sciences	Hungary	TTK IF-28/201
Hungarian Academy of Sciences	Hungary	MedinProt program
European Union		283570

Revision History  

• Version 1.0: 2015-12-23
  Type: Initial release
  
• Version 2.0: 2024-01-10
  Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description