3ZF6

Phage dUTPases control transfer of virulence genes by a proto-oncogenic G protein-like mechanism. (Staphylococcus bacteriophage 80alpha dUTPase D81A D110C S168C mutant with dUpNHpp).

Structural Biology Knowledgebase: 3ZF6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.224

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3ZF6

Classification: HYDROLASE

Total Structure Weight: 23053.48

Macromolecule Entities
Molecule Chains Length Organism Details
DUTPASE A 204 Staphylococcus phage 80alpha EC#: 3.6.1.23 IUBMB
Mutation: D81A, D110C, S168C
Details: STRUCTURE IN PRESENCE OF DUMP
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 2'-DEOXYURIDINE 5'-MONOPHOSPHATE
DUMP (Synonym)
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-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: 2.6 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.224
  • Space Group: P 21 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 87.46 α = 90.00
b = 87.46 β = 90.00
c = 87.46 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: Other | Details: REMARK 465
  • 2013-04-17
    Type: Polymer description | Details: SEQRES
  • 2013-04-17
    Type: Sequence database correspondence | Details: SEQADV
  • 2013-04-03
    Type: Refinement description | Details: REMARK 3
  • 2013-04-03
    Type: Entry title | Details: TITLE
  • 2013-04-03
    Type: Other | Details: REMARK 900
  • 2013-03-20
    Type: Citation | Details: JRNL