3ZF4

Phage dUTPases control transfer of virulence genes by a proto- oncogenic G protein-like mechanism. (Staphylococcus bacteriophage 80alpha dUTPase Y81A mutant with dUpNHpp).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.291
  • R-Value Work: 0.240

Literature

Macromolecules
Sequence Display for 3ZF4

Classification: HYDROLASE

Total Structure Weight: 23184.38

Macromolecule Entities
Molecule Chains Length Organism Details
DUTPASE A 204 Staphylococcus phage 80alpha EC#: 3.6.1.23 IUBMB
Mutation: Y84A
Details: STRUCTURE IN PRESENCE OF DUPNHPP AND MAGNESIUM
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DUP
Query on DUP

A 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
C9 H16 N3 O13 P3
XZLLMTSKYYYJLH-SHYZEUOFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

A NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.291
  • R-Value Work: 0.240
  • Space Group: P 21 3

Unit Cell:

Length (Å) Angle (°)
a = 87.47 α = 90.00
b = 87.47 β = 90.00
c = 87.47 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-12-10
  • Released Date: 2013-01-30
  • Deposition author(s): Tormo-Mas, M.A., Donderis, J., Garcia-Caballer, M., Alt, A., Mir-Sanchis, I., Marina, A., Penades, J.R.

Revision History

  • 2013-03-20
    Type: Database references
  • 2013-04-03
    Type: Other, Refinement description, Structure summary
  • 2013-04-17
    Type: Database references, Other, Structure summary