3EA6 | pdb_00003ea6

Atomic resolution of crystal structure of SEK

• PDB DOI: https://doi.org/10.2210/pdb3EA6/pdb

• Classification: TOXIN
• Organism(s): Staphylococcus aureus
• Mutation(s): No 


• Deposited: 2008-08-24 Released: 2009-06-30 
• Deposition Author(s): Shi, K., Huseby, M., Schlievert, P.M., Ohlendorf, D.H., Earhart, C.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.92 Å
• R-Value Free: 
  0.122 (Depositor) 
• R-Value Work: 
  0.101 (Depositor), 0.106 (DCC) 
• R-Value Observed: 
  0.101 (Depositor) 

Starting Model: experimental

Literature

Structural Studies of an Emerging Pyrogenic Superantigen, SEK

Shi, K., Huseby, M., Schlievert, P.M., 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)

Macromolecule Content 

• Total Structure Weight: 26.07 kDa 
• Atom Count: 2,292 
• Modeled Residue Count: 215 
• Deposited Residue Count: 219 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Staphylococcal enterotoxin K	A	219	Staphylococcus aureus	Mutation(s): 0  Gene Names: sek, SACOL0886
UniProt
Find proteins for Q93CC5 (Staphylococcus aureus) Explore Q93CC5  Go to UniProtKB:  Q93CC5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.92 Å
• R-Value Free:  0.122 (Depositor) 
• R-Value Work:  0.101 (Depositor), 0.106 (DCC) 
• R-Value Observed: 0.101 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.829	α = 90
b = 53.652	β = 90
c = 92.94	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-30 
Deposition Author(s): Shi, K., Huseby, M., Schlievert, P.M., Ohlendorf, D.H., Earhart, C.A.

Revision History  

• Version 1.0: 2009-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description