4E1C | pdb_00004e1c

Structure of a VgrG Vibrio cholerae toxin ACD domain in complex with ADP and Mg++

• PDB DOI: https://doi.org/10.2210/pdb4E1C/pdb

• Classification: TOXIN
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-03-06 Released: 2012-08-29 
• Deposition Author(s): Durand, E., Audoly, G., Derrez, E., Spinelli, S., Ortiz-Lombardia, M., Cascales, E., Raoult, D., Cambillau, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.196 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Structure and functional characterization of the Vibrio cholerae toxin from the VgrG/MARTX family.

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

(2012) J Biological Chem 

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: 44.69 kDa 
• Atom Count: 3,296 
• Modeled Residue Count: 356 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VgrG protein	A	396	Vibrio cholerae	Mutation(s): 0  Gene Names: VC_1416, VgrG1 EC: 6.3.2
UniProt
Find proteins for A0A0H3AIG7 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A0A0H3AIG7  Go to UniProtKB:  A0A0H3AIG7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
SO4	F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.196 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.46	α = 90
b = 128.46	β = 90
c = 76.39	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
BUSTER	refinement
HKL-3000	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): Durand, E., Audoly, G., Derrez, E., Spinelli, S., Ortiz-Lombardia, M., Cascales, E., Raoult, D., Cambillau, C.

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description