4XZK | pdb_00004xzk

Crystal structure of ADP-ribosyltransferase Vis in complex with agmatine

• PDB DOI: https://doi.org/10.2210/pdb4XZK/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio splendidus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-02-04 Released: 2016-01-20 
• Deposition Author(s): Pfoh, R., Ravulapalli, R., Merrill, A.R., Pai, E.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.221 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 27.17 kDa 
• Atom Count: 1,817 
• Modeled Residue Count: 215 
• Deposited Residue Count: 239 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative NAD(+)--arginine ADP-ribosyltransferase Vis	A	239	Vibrio splendidus	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AG2	B [auth A]	AGMATINE C5 H14 N4 QYPPJABKJHAVHS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.221 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.84	α = 90
b = 52.09	β = 90
c = 102.87	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PDB_EXTRACT	data extraction
REFMAC	refinement
XPREP	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Pfoh, R., Ravulapalli, R., Merrill, A.R., Pai, E.F.

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description