8U2F | pdb_00008u2f

Vibrio parahaemolyticus ToxS periplasmic domain

• PDB DOI: https://doi.org/10.2210/pdb8U2F/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Vibrio parahaemolyticus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2023-09-06 Released: 2024-09-11 
• Deposition Author(s): Kim, M., Kull, F.J., Midgett, C.R.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.263 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: in silico

Literature

Vibrio parahaemolyticus ToxS periplasmic domain

Kim, M., Kull, F.J., Midgett, C.R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.69 kDa 
• Atom Count: 2,288 
• Modeled Residue Count: 274 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane regulatory protein ToxS	A, B	149	Vibrio parahaemolyticus	Mutation(s): 0  Gene Names: toxS
UniProt
Find proteins for Q05939 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q05939  Go to UniProtKB:  Q05939

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.263 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.85	α = 90
b = 58.33	β = 90
c = 89.68	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-11 
Deposition Author(s): Kim, M., Kull, F.J., Midgett, C.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2024-09-11
  Type: Initial release