4GQK

Structure of Native VgrG1-ACD with ADP (no cations)

• PDB DOI: https://doi.org/10.2210/pdb4GQK/pdb

• Classification: PROTEIN BINDING
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-08-23 Released: 2013-09-25 
• Deposition Author(s): Nguyen, V.S., Spinelli, S., Derrez, E., Durand, E., Cambillau, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.217 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 

Literature

Structure of Native VgrG1-ACD with ADP (no cations)

Nguyen, V.S., Spinelli, S., Derrez, E., Durand, E., Cambillau, C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.3 kDa 
• Atom Count: 3,267 
• Modelled 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 O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: VC_1416, VgrG1
UniProt
Find proteins for Q9KS45 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KS45  Go to UniProtKB:  Q9KS45

Small Molecules

Ligands 2 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	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.217 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 
• Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.71	α = 90
b = 128.71	β = 90
c = 76.59	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-25 
Deposition Author(s): Nguyen, V.S., Spinelli, S., Derrez, E., Durand, E., Cambillau, C.

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description