1SE3 | pdb_00001se3

STAPHYLOCOCCAL ENTEROTOXIN B COMPLEXED WITH GM3 TRISACCHARIDE

• PDB DOI: https://doi.org/10.2210/pdb1SE3/pdb

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


• Deposited: 1996-10-11 Released: 1997-06-16 
• Deposition Author(s): Swaminathan, S., Sax, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.330 (Depositor) 
• R-Value Work: 
  0.220 (Depositor) 
• R-Value Observed: 
  0.220 (Depositor) 

Literature

Residues defining V beta specificity in staphylococcal enterotoxins.

Swaminathan, S., Furey, W., Pletcher, J., Sax, M.

(1995) Nat Struct Biol 2: 680-686

• PubMed: 7552730 
• DOI: https://doi.org/10.1038/nsb0895-680
• Primary Citation Related Structures: 
  1SE2, 1SE3, 1SE4


• PubMed Abstract: 
  

  The three-dimensional structure of staphylococcal enterotoxin C2 has been determined at 2.7 A resolution by x-ray diffraction, while the structures of enterotoxins A and E have been modelled based on their sequence homology to other staphylococcal enterotoxins. The T-cell receptor-binding sites of staphylococcal enterotoxin (SE) B and SEC2 are compared and the stereochemical interactions likely to be responsible for their differing V beta specificities are identified. A similar comparison is made between SEA and SEE.

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Organizational Affiliation: 
• Biocrystallography Laboratory, VA Medical Center, Pittsburgh, Pennsylvania 15240, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.04 kDa 
• Atom Count: 2,153 
• Modeled Residue Count: 239 
• Deposited Residue Count: 239 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STAPHYLOCOCCAL ENTEROTOXIN B	A	239	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for P01552 (Staphylococcus aureus) Explore P01552  Go to UniProtKB:  P01552

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan: G91237TK GlyCosmos: G91237TK GlyGen: G91237TK

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.330 (Depositor) 
• R-Value Work:  0.220 (Depositor) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.3	α = 90
b = 71	β = 90
c = 78.4	γ = 90

Software Package:

Software Name	Purpose
XENGEN	data collection
FBSCALE	data reduction
X-PLOR	model building
X-PLOR	refinement
XENGEN	data reduction
FBSCALE	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-06-16 
Deposition Author(s): Swaminathan, S., Sax, M.

Revision History  

• Version 1.0: 1997-06-16
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2024-10-30
  Changes: Data collection, Database references, Structure summary