4DTF

Structure of a VgrG Vibrio cholerae toxin ACD domain in complex with AMP-PNP and Mg++


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure of a VgrG Vibrio cholerae toxin ACD domain in complex with AMP-PNP and Mg++

Durand, E.Audoly, G.Derrez, E.Spinelli, S.Ortiz-Lombardia, M.Cascales, E.Raoult, D.Cambillau, C.

(2012) J.Biol.Chem. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VgrG protein
A
396Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)Gene Names: vgrG1 (vgrG-1)
EC: 6.3.2.-
Find proteins for A0A0H3AIG7 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395))
Go to UniProtKB:  A0A0H3AIG7
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ANP
Query on ANP

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Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.177 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 128.390α = 90.00
b = 128.390β = 90.00
c = 76.580γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
MAR345dtbdata collection
MOLREPphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-29
    Type: Initial release