3ZF1

Phage dUTPases control transfer of virulence genes by a proto- oncogenic G protein-like mechanism. (Staphylococcus bacteriophage 80alpha dUTPase D81N mutant with dUpNHpp).

Structural Biology Knowledgebase: 3ZF1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.285
  • R-Value Work: 0.230

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3ZF1

Classification: HYDROLASE

Total Structure Weight: 23251.36

Macromolecule Entities
Molecule Chains Length Organism Details
DUTPASE A 204 Staphylococcus phage 80alpha EC#: 3.6.1.23 IUBMB
Mutation: D81N
Details: STRUCTURE IN PRESENCE OF DUPNHPP AND MAGNESIUM
Gene Name(s):

Small Molecules
Ligands 2 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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.285
  • R-Value Work: 0.230
  • Space Group: P 21 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 87.21 α = 90.00
b = 87.21 β = 90.00
c = 87.21 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

  • 2013-04-17
    Type: Polymer description | Details: SEQRES
  • 2013-04-17
    Type: Sequence database correspondence | Details: SEQADV
  • 2013-04-17
    Type: Other | Details: REMARK 465
  • 2013-04-03
    Type: Other | Details: REMARK 900
  • 2013-04-03
    Type: Refinement description | Details: REMARK 3
  • 2013-04-03
    Type: Entry title | Details: TITLE
  • 2013-03-20
    Type: Citation | Details: JRNL