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- PDB-3seb: STAPHYLOCOCCAL ENTEROTOXIN B -

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Basic information

Entry
Database: PDB / ID: 3seb
TitleSTAPHYLOCOCCAL ENTEROTOXIN B
ComponentsSTAPHYLOCOCCAL ENTEROTOXIN B
KeywordsTOXIN / SUPERANTIGEN / ENTEROTOXIN
Function / homology
Function and homology information


toxin activity / extracellular region / metal ion binding
Similarity search - Function
Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Ubiquitin-like (UB roll) - #120 / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain ...Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Ubiquitin-like (UB roll) - #120 / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Superantigen toxin, C-terminal / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsPapageorgiou, A.C. / Acharya, K.R.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of microbial superantigen staphylococcal enterotoxin B at 1.5 A resolution: implications for superantigen recognition by MHC class II molecules and T-cell receptors.
Authors: Papageorgiou, A.C. / Tranter, H.S. / Acharya, K.R.
#1: Journal: Structure / Year: 1997
Title: Superantigens as Immunomodulators: Recent Structural Insights
Authors: Papageorgiou, A.C. / Acharya, K.R.
#2: Journal: Structure / Year: 1995
Title: Crystal Structure of the Superantigen Enterotoxin C2 from Staphylococcus Aureus Reveals a Zinc-Binding Site
Authors: Papageorgiou, A.C. / Acharya, K.R. / Shapiro, R. / Passalacqua, E.F. / Brehm, R.D. / Tranter, H.S.
History
DepositionNov 26, 1997Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STAPHYLOCOCCAL ENTEROTOXIN B


Theoretical massNumber of molelcules
Total (without water)28,2821
Polymers28,2821
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.404, 67.720, 79.065
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein STAPHYLOCOCCAL ENTEROTOXIN B / SEB


Mass: 28281.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: P01552
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal
*PLUS
Density % sol: 2.05 %
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %(w/v)PEG33501reservoir
20.02 %(w/v)sodium azide1reservoir
30.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 5, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 38513 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 12.5
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 3.6 / % possible all: 79.9
Reflection
*PLUS
Num. measured all: 389081
Reflection shell
*PLUS
% possible obs: 79.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97model building
SHELXL-97refinement
SHELXL-97phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SEB IN COMPLEX WITH AN MHC CLASS-II MOLECULE.

Resolution: 1.48→20 Å / Num. parameters: 8551 / Num. restraintsaints: 7996 / Stereochemistry target values: ENGH AND HUBER
Details: INITIAL REFINEMENT WAS CARRIED OUT WITH X-PLOR 3.1. THE LAST RECORDED R-FREE (5% OF THE REFLECTIONS EXCLUDED FROM THE REFINEMENT) WAS 0.252. AT THIS STAGE THE PROGRAM SHELXL-97 WAS EMPLOYED ...Details: INITIAL REFINEMENT WAS CARRIED OUT WITH X-PLOR 3.1. THE LAST RECORDED R-FREE (5% OF THE REFLECTIONS EXCLUDED FROM THE REFINEMENT) WAS 0.252. AT THIS STAGE THE PROGRAM SHELXL-97 WAS EMPLOYED FOR THE REMAINDER OF THE REFINEMENT. ALL DATA WERE USED. A POSTERIORI R-FREE CALCULATION GAVE AN R-FREE OF 0.209 WITH X-PLOR.
RfactorNum. reflection
obs0.1817 -
all-38476
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2137
Refinement stepCycle: LAST / Resolution: 1.48→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 0 177 2125
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d1.73
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg27.42
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg1.29

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