3B79

Crystal structure of the N-terminal peptidase C39 like domain of the toxin secretion ATP-binding protein from Vibrio parahaemolyticus

• PDB DOI: https://doi.org/10.2210/pdb3B79/pdb

• Classification: NUCLEOTIDE BINDING PROTEIN
• Organism(s): Vibrio parahaemolyticus RIMD 2210633
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-10-30 Released: 2007-11-13 
• Deposition Author(s): Kim, Y., Li, H., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 0.182 
• R-Value Work: 0.155 
• R-Value Observed: 0.158 

Literature

Crystal structure of the N-terminal peptidase C39 like domain of the toxin secretion ATP-binding protein from Vibrio parahaemolyticus.

Kim, Y., Li, H., Abdullah, J., Joachimiak, A.

To be published.

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: 14.34 kDa 
• Atom Count: 1,327 
• Modelled Residue Count: 125 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toxin secretion ATP-binding protein	A	129	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 0  Gene Names: VPA1736
UniProt
Find proteins for Q87FE3 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87FE3  Go to UniProtKB:  Q87FE3

Small Molecules

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: 1.37 Å
• R-Value Free: 0.182 
• R-Value Work: 0.155 
• R-Value Observed: 0.158 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.173	α = 90
b = 46.173	β = 90
c = 105.975	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELX	phasing
MLPHARE	phasing
RESOLVE	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-13 
Deposition Author(s): Kim, Y., Li, H., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-11-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance