4XZK

Crystal structure of ADP-ribosyltransferase Vis in complex with agmatine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Vis toxin, an ADP-ribosyltransferase from Vibrio splendidus

Ravulapalli, R.Visschedyk, D.Pfoh, R.Logo, M.Fieldhouse, R.J.Pai, E.F.Merrill, A.R.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative NAD(+)--arginine ADP-ribosyltransferase VisA239Vibrio splendidusMutation(s): 0 
Gene Names: V12B01_18061
EC: 2.4.2.31
UniProt
Find proteins for A3UNN4 (Vibrio splendidus (strain 12B01))
Explore A3UNN4 
Go to UniProtKB:  A3UNN4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3UNN4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AG2
Query on AG2

Download Ideal Coordinates CCD File 
B [auth A]AGMATINE
C5 H14 N4
QYPPJABKJHAVHS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.84α = 90
b = 52.09β = 90
c = 102.87γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement
XPREPdata reduction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Derived calculations, Refinement description