3KI0

Catalytic fragment of Cholix toxin from Vibrio Cholerae in complex with inhibitor GP-D

• PDB DOI: https://doi.org/10.2210/pdb3KI0/pdb

• Classification: Transferase,toxin
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-31 Released: 2010-10-27 
• Deposition Author(s): Jorgensen, R., Edwards, P.R., Merrill, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Structure function analysis of soluble inhibitors of cholix toxin from Vibrio cholerae

Jorgensen, R., Edwards, P.R., 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: 23.94 kDa 
• Atom Count: 1,958 
• Modelled Residue Count: 199 
• Deposited Residue Count: 211 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholix toxin	A	211	Vibrio cholerae	Mutation(s): 0  Gene Names: chxa, toxA EC: 2.4.2.36
UniProt
Find proteins for Q5EK40 (Vibrio cholerae) Explore Q5EK40  Go to UniProtKB:  Q5EK40

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G9D	B [auth A], C [auth A]	3-(morpholin-4-ylmethyl)-1,5-dihydro-6H-[1,2]diazepino[4,5,6-cd]indol-6-one C15 H16 N4 O2 VLZMFVRHOYPDFA-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.45	α = 90
b = 64.89	β = 90
c = 78.48	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Macromolecular	data collection
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-27 
Deposition Author(s): Jorgensen, R., Edwards, P.R., Merrill, A.R.

Revision History  

• Version 1.0: 2010-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description