3GK6

Crystal structure from the mobile metagenome of Vibrio cholerae. Integron cassette protein VCH_CASS2.

• PDB DOI:  https://doi.org/10.2210/pdb3GK6/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-10 Released: 2009-03-24 
• Deposition Author(s): Deshpande, C.N., Sureshan, V., Harrop, S.J., Boucher, Y., Xu, X., Cui, H., Edwards, A.M., Savchenko, A., Joachimiak, A., Chang, C., Stokes, H.W., Curmi, P.M.G., Mabbutt, B.C., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.227 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Literature

Crystal Structure of an Integron Gene Cassette-Associated Protein from Vibrio cholerae Identifies a Cationic Drug-Binding Module.

Deshpande, C.N., Harrop, S.J., Boucher, Y., Hassan, K.A., Leo, R.D., Xu, X., Cui, H., Savchenko, A., Chang, C., Labbate, M., Paulsen, I.T., Stokes, H.W., Curmi, P.M., Mabbutt, B.C.

(2011) PLoS One 6: e16934-e16934

• PubMed: 21390267 
• DOI: https://doi.org/10.1371/journal.pone.0016934
• Primary Citation of Related Structures:  
  3GK6


• PubMed Abstract: 
  

The direct isolation of integron gene cassettes from cultivated and environmental microbial sources allows an assessment of the impact of the integron/gene cassette system on the emergence of new phenotypes, such as drug resistance or virulence. A structural approach is being exploited to investigate the modularity and function of novel integron gene cassettes.

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Organizational Affiliation: 

Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia.

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: 19.84 kDa 
• Atom Count: 1,375 
• Modelled Residue Count: 153 
• Deposited Residue Count: 170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integron cassette protein VCH_CASS2	A	170	Vibrio cholerae	Mutation(s): 0  Gene Names: OPVCH_OP4G
UniProt
Find proteins for D0VX23 (Vibrio cholerae) Explore D0VX23  Go to UniProtKB:  D0VX23

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE4	B [auth A]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C16 H34 O8 PJWQOENWHPEPKI-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.227 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.378	α = 90
b = 59.378	β = 90
c = 95.756	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
AutoSol	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-24 
Deposition Author(s): Deshpande, C.N., Sureshan, V., Harrop, S.J., Boucher, Y., Xu, X., Cui, H., Edwards, A.M., Savchenko, A., Joachimiak, A., Chang, C., Stokes, H.W., Curmi, P.M.G., Mabbutt, B.C., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-03-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance