3URY | pdb_00003ury

Crystal Structure of Superantigen-like Protein, Exotoxin from Staphylococcus aureus subsp. aureus NCTC 8325

• PDB DOI: https://doi.org/10.2210/pdb3URY/pdb

• Classification: TOXIN
• Organism(s): Staphylococcus aureus subsp. aureus NCTC 8325
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-11-22 Released: 2011-12-28 
• Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Halavaty, A., Winsor, J., Dubrovska, I., Bagnoli, F., Falugi, F., Bottomley, M., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.247 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Superantigen-like Protein, Exotoxin from Staphylococcus aureus subsp. aureus NCTC 8325

Filippova, E.V., Minasov, G., Shuvalova, L., Halavaty, A., Winsor, J., Dubrovska, I., Bagnoli, F., Falugi, F., Bottomley, M., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 6 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.77 kDa 
• Atom Count: 3,244 
• Modeled Residue Count: 386 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exotoxin	A, B	193	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0  Gene Names: SAOUHSC_00389
UniProt
Find proteins for Q2G1S8 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G1S8  Go to UniProtKB:  Q2G1S8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth A], E [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.247 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33ury

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.734	α = 90
b = 79.555	β = 103.16
c = 55.354	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
BALBES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-28 
Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Halavaty, A., Winsor, J., Dubrovska, I., Bagnoli, F., Falugi, F., Bottomley, M., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-12-28
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description