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- PDB-1esf: STAPHYLOCOCCAL ENTEROTOXIN A -

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Basic information

Entry
Database: PDB / ID: 1esf
TitleSTAPHYLOCOCCAL ENTEROTOXIN A
ComponentsSTAPHYLOCOCCAL ENTEROTOXIN A
KeywordsENTEROTOXIN / STAPHYLOCOCCAL ENTEROTOXIN TYPE A
Function / homology
Function and homology information


MHC class II protein binding / 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
: / Enterotoxin type A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsSchad, E.M. / Svensson, L.A.
Citation
Journal: EMBO J. / Year: 1995
Title: Crystal structure of the superantigen staphylococcal enterotoxin type A.
Authors: Schad, E.M. / Zaitseva, I. / Zaitsev, V.N. / Dohlsten, M. / Kalland, T. / Schlievert, P.M. / Ohlendorf, D.H. / Svensson, L.A.
#1: Journal: Embo J. / Year: 1995
Title: Characterization of Two Distinct Mhc Class II Binding Sites in the Superantigen Staphylococcal Enterotoxin A
Authors: Abrahmsen, L. / Dohlsten, M. / Segren, S. / Bjork, P. / Jonsson, E. / Kalland, T.
#2: Journal: Nature / Year: 1994
Title: Three-Dimensional Structure of a Human Class II Histocompatibility Molecule Complexed with Superantigen
Authors: Jardetzky, T.S. / Brown, J.H. / Gorga, J.C. / Stern, L.J. / Urban, R.G. / Chi, Y.I. / Stauffacher, C. / Strominger, J.L. / Wiley, D.C.
#3: Journal: Biochemistry / Year: 1993
Title: Structure of Toxic Shock Syndrome Toxin 1
Authors: Prasad, G.S. / Earhart, C.A. / Murray, D.L. / Novick, R.P. / Schlievert, P.M. / Ohlendorf, D.H.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Zinc Regulates the Function of Two Superantigens
Authors: Fraser, J.D. / Urban, R.G. / Strominger, J.L. / Robinson, H.
#5: Journal: Nature / Year: 1992
Title: Crystal Structure of Staphylococcal Enterotoxin B, a Superantigen
Authors: Swaminathan, S. / Furey, W. / Pletcher, J. / Sax, M.
History
DepositionMay 25, 1995Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STAPHYLOCOCCAL ENTEROTOXIN A
B: STAPHYLOCOCCAL ENTEROTOXIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4854
Polymers54,2612
Non-polymers2252
Water3,027168
1
A: STAPHYLOCOCCAL ENTEROTOXIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2432
Polymers27,1301
Non-polymers1121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: STAPHYLOCOCCAL ENTEROTOXIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2432
Polymers27,1301
Non-polymers1121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.600, 62.500, 75.100
Angle α, β, γ (deg.)90.00, 96.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.997839, -0.064848, 0.010615), (-0.064725, -0.997836, -0.011541), (0.011341, 0.010829, -0.999877)
Vector: 23.42651, 27.2472, 37.36518)

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Components

#1: Protein STAPHYLOCOCCAL ENTEROTOXIN A


Mass: 27130.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A0L2
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.64 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlprotein1drop
220 mMTricine1drop
30.060 mM1dropCdSO4
420 %PEG40001reservoir
5250 mMMES1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 18, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→29 Å / Num. obs: 37509 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.044 / Rsym value: 0.064

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.277 -10 %
Rwork0.204 --
obs0.204 37509 -
Displacement parametersBiso mean: 30.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3747 0 4 169 3920
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.056
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.87
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.744
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.871
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.744

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