3I46 | pdb_00003i46

Crystal structure of beta toxin from Staphylococcus aureus F277A, P278A mutant with bound calcium ions

• PDB DOI: https://doi.org/10.2210/pdb3I46/pdb

• Classification: TOXIN
• Organism(s): Staphylococcus aureus subsp. aureus RN4220
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-07-01 Released: 2010-07-14 
• 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: 2.60 Å
• R-Value Free: 
  0.275 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

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)

Macromolecule Content 

• Total Structure Weight: 72.42 kDa 
• Atom Count: 4,685 
• Modeled Residue Count: 578 
• Deposited Residue Count: 634 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-hemolysin	A, B	317	Staphylococcus aureus subsp. aureus RN4220	Mutation(s): 2  Gene Names: hlb
UniProt
Find proteins for A7LAI8 (Staphylococcus aureus) Explore A7LAI8  Go to UniProtKB:  A7LAI8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A], G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.275 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.093	α = 90
b = 70.195	β = 90
c = 129.584	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-14 
Deposition Author(s): Huseby, M., Shi, K., Kruse, A.C., Ohlendorf, D.H.

Revision History  

• Version 1.0: 2010-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.3: 2024-04-03
  Changes: Data collection, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary