3KI4 | pdb_00003ki4

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

• PDB DOI: https://doi.org/10.2210/pdb3KI4/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: 1.65 Å
• R-Value Free: 
  0.202 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.169 (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: 23.84 kDa 
• Atom Count: 1,865 
• Modeled 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
G9P	B [auth A]	(11bR)-3-oxo-1,2,3,11b-tetrahydrochromeno[4,3,2-de]isoquinoline-10-sulfonic acid C15 H11 N O5 S XIIAPOBAFRAUGJ-LLVKDONJSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.202 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.525	α = 90
b = 64.685	β = 90
c = 84.226	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MX	data collection
HKL-2000	data reduction
HKL-2000	data scaling

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: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description