4G54

Crystal structure of a periplasmic domain of the EpsAB fusion protein of the Vibrio vulnificus type II secretion system

• PDB DOI: https://doi.org/10.2210/pdb4G54/pdb

• Classification: Peptidoglycan-binding protein
• Organism(s): Vibrio vulnificus
• Mutation(s): No 


• Deposited: 2012-07-17 Released: 2013-01-30 
• Deposition Author(s): Martynnowski, D., Grochulski, P., Howard, S.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.202 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 

Literature

Structure of a periplasmic domain of the EpsAB fusion protein of the Vibrio vulnificus type II secretion system.

Martynowski, D., Grochulski, P., Howard, P.S.

(2013) Acta Crystallogr D Biol Crystallogr 69: 142-149

• PubMed: 23385451 
• DOI: https://doi.org/10.1107/S0907444912042710
• Primary Citation of Related Structures:  
  4G54


• PubMed Abstract: 
  

  Vibrio vulnificus utilizes the type II secretion system (T2SS), culminating in a megadalton outer membrane complex called the secretin, to translocate extracellular proteins from the periplasmic space across the outer membrane. In Aeromonas hydrophila, the general secretion pathway proteins ExeA and ExeB form an inner membrane complex which interacts with peptidoglycan and is required for the assembly of the secretin composed of ExeD. In V. vulnificus, these two proteins are fused into one protein, EpsAB. Here, the crystal structure of a periplasmic domain of EpsAB (amino acids 333-584) solved by SAD phasing is presented. The crystals belonged to space group C2 and diffracted to 1.55 Å resolution.

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Organizational Affiliation: 

Department of Microbiology and Immunology, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 2W8, Canada.

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: 29.87 kDa 
• Atom Count: 2,082 
• Modelled Residue Count: 222 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
General Secretion Pathway Protein	A	258	Vibrio vulnificus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.202 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.821	α = 90
b = 44.523	β = 110.59
c = 51.04	γ = 90

Software Package:

Software Name	Purpose
MsDC	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-30 
Deposition Author(s): Martynnowski, D., Grochulski, P., Howard, S.P.

Revision History  

• Version 1.0: 2013-01-30
  Type: Initial release
  
• Version 1.1: 2013-03-27
  Changes: Database references
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Structure summary