1YC9

The crystal structure of the outer membrane protein VceC from the bacterial pathogen Vibrio cholerae at 1.8 resolution

• PDB DOI: https://doi.org/10.2210/pdb1YC9/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2004-12-22 Released: 2005-03-01 
• Deposition Author(s): Federici, L., Du, D., Walas, F., Matsumura, H., Fernandez-Recio, J., McKeegan, K.S., Borges-Walmsley, M.I., Luisi, B.F., Walmsley, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.221 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 48.38 kDa 
• Atom Count: 3,488 
• Modelled Residue Count: 411 
• Deposited Residue Count: 442 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
multidrug resistance protein	A	442	Vibrio cholerae	Mutation(s): 1  Membrane Entity: Yes
UniProt
Find proteins for Q9KS51 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KS51  Go to UniProtKB:  Q9KS51

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BOG	B [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
HG	C [auth A], D [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.221 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.458	α = 90
b = 71.458	β = 90
c = 190.702	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-01 
Deposition Author(s): Federici, L., Du, D., Walas, F., Matsumura, H., Fernandez-Recio, J., McKeegan, K.S., Borges-Walmsley, M.I., Luisi, B.F., Walmsley, A.R.

Revision History  

• Version 1.0: 2005-03-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2021-11-10
  Changes: Advisory, Database references, Structure summary