3V05 | pdb_00003v05

2.4 Angstrom Crystal Structure of Superantigen-like Protein from Staphylococcus aureus.

• PDB DOI: https://doi.org/10.2210/pdb3V05/pdb

• Classification: TOXIN
• Organism(s): Staphylococcus aureus subsp. aureus NCTC 8325
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-12-07 Released: 2011-12-21 
• Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Filippova, E.V., Dubrovska, I., Winsor, J., 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: 2.40 Å
• R-Value Free: 
  0.260 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

2.4 Angstrom Crystal Structure of Superantigen-like Protein from Staphylococcus aureus.

Minasov, G., Halavaty, A., Shuvalova, L., Filippova, E.V., Dubrovska, I., Winsor, J., 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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 102.72 kDa 
• Atom Count: 6,613 
• Modeled Residue Count: 764 
• Deposited Residue Count: 872 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superantigen-like Protein	A, B, C, D	218	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0  Gene Names: SAOUHSC_00391
UniProt
Find proteins for Q2G1S5 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G1S5  Go to UniProtKB:  Q2G1S5

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.260 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33v05

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.64	α = 90
b = 106.504	β = 90
c = 162.085	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-21 
Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Filippova, E.V., Dubrovska, I., Winsor, J., Bagnoli, F., Falugi, F., Bottomley, M., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-12-21
  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