3I5V

Crystal structure of beta toxin 275-280 from Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb3I5V/pdb

• Classification: TOXIN
• Organism(s): Staphylococcus aureus subsp. aureus RN4220
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-06 Released: 2010-08-11 
• Deposition Author(s): Huseby, M., Shi, K., Kruse, A.C., Ohlendorf, D.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.267 
• R-Value Work: 0.214 
• R-Value Observed: 0.214 

Starting Model: experimental

Literature

Structure and biological functions of beta toxin from Staphylococcus aureus: Role of the hydrophobic beta hairpin in virulence

Huseby, M., Shi, K., Kruse, A.C., Digre, J., Mengistu, F., Bohach, G.A., Schlievert, P.S., Ohlendorf, D.H., Earhart, C.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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 142.87 kDa 
• Atom Count: 9,255 
• Modelled Residue Count: 1,139 
• Deposited Residue Count: 1,252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-hemolysin	A, B, C, D	313	Staphylococcus aureus subsp. aureus RN4220	Mutation(s): 0  Gene Names: hlb EC: 3.1.4.3
UniProt
Find proteins for P09978 (Staphylococcus aureus) Explore P09978  Go to UniProtKB:  P09978

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGA	E [auth D]	DIACYL GLYCEROL C39 H76 O5 UHUSDOQQWJGJQS-QNGWXLTQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.267 
• R-Value Work: 0.214 
• R-Value Observed: 0.214 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.184	α = 93.06
b = 69.053	β = 94.6
c = 75.654	γ = 92.13

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-11 
Deposition Author(s): Huseby, M., Shi, K., Kruse, A.C., Ohlendorf, D.H.

Revision History  

• Version 1.0: 2010-08-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary