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- PDB-1exf: EXFOLIATIVE TOXIN A -

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Basic information

Entry
Database: PDB / ID: 1exf
TitleEXFOLIATIVE TOXIN A
ComponentsEXFOLIATVE TOXIN A
KeywordsCOMPLEX (TOXIN/PEPTIDE) / COMPLEX (TOXIN-PEPTIDE) / HYDROLASE / SERINE PROTEASE / SUPERANTIGEN / COMPLEX (TOXIN-PEPTIDE) complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / toxin activity / serine-type endopeptidase activity / proteolysis
Similarity search - Function
Serine proteases, V8 family, serine active site / Serine proteases, V8 family, serine active site. / Serine proteases, V8 family, histidine active site / Serine proteases, V8 family, histidine active site. / Peptidase S1B, exfoliative toxin / Peptidase S1B / Trypsin-like peptidase domain / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold ...Serine proteases, V8 family, serine active site / Serine proteases, V8 family, serine active site. / Serine proteases, V8 family, histidine active site / Serine proteases, V8 family, histidine active site. / Peptidase S1B, exfoliative toxin / Peptidase S1B / Trypsin-like peptidase domain / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
GLYCINE / Exfoliative toxin A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsVath, G.M. / Earhart, C.A. / Rago, J.V. / Kim, M.H. / Bohach, G.A. / Schlievert, P.M. / Ohlendorf, D.H.
CitationJournal: Biochemistry / Year: 1997
Title: The structure of the superantigen exfoliative toxin A suggests a novel regulation as a serine protease.
Authors: Vath, G.M. / Earhart, C.A. / Rago, J.V. / Kim, M.H. / Bohach, G.A. / Schlievert, P.M. / Ohlendorf, D.H.
History
DepositionOct 22, 1996Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Category: entity_src_nat

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EXFOLIATVE TOXIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0602
Polymers26,9851
Non-polymers751
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.500, 71.500, 122.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein EXFOLIATVE TOXIN A / ETA


Mass: 26985.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: MNEV
References: UniProt: P09331, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
Details: GLYCINE WAS MODELED INTO TO A STRONG FO-FC FEATURE DUE TO THE SHAPE AND ENVIRONMENT OF THE FEATURE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Compound detailsETA IS STRUCTURALLY HOMOLOGOUS TO THE CHYMOTRYPSIN-LIKE SERINE PROTEASES. PEPTIDE BOND CLEAVAGE, ...ETA IS STRUCTURALLY HOMOLOGOUS TO THE CHYMOTRYPSIN-LIKE SERINE PROTEASES. PEPTIDE BOND CLEAVAGE, HOWEVER, HAS NOT BEEN DEMONSTRATED. ETA IS MITOGENIC FOR T LYMPHOCYTES AND REPORTED TO BE A SUPERANTIGEN.
Sequence detailsETA NUMBERING BASED ON STRUCTURAL SIMILARITY TO CHYMOTRYPSIN (W.BODE ET AL., 1989, EMBO J. 8,3467-3475).

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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: 2.91 Å3/Da / Density % sol: 57.71 % / Description: REFINEMENT INCLUDED BULK SOLVENT CORRECTION.
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
2100 mMcacodylate1drop
329 %PEG80001drop
4200 mMammonium sulfate1drop
5100 mMcacodylate1reservoir
629 %PEG80001reservoir
7200 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 15, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→17 Å / Num. obs: 16869 / % possible obs: 87.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.0723

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Processing

Software
NameVersionClassification
XENGENdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.1→17 Å / σ(F): 0
Details: GLY 300: GLYCINE WAS MODELED INTO TO A STRONG FO-FC FEATURE DUE TO THE SHAPE AND ENVIRONMENT OF THE FEATURE THE SIDE CHAINS OF RESIDUES GLU 1E, GLU1F, AND ARG 221A WERE NOT VISIBLE BEYOND CB. ...Details: GLY 300: GLYCINE WAS MODELED INTO TO A STRONG FO-FC FEATURE DUE TO THE SHAPE AND ENVIRONMENT OF THE FEATURE THE SIDE CHAINS OF RESIDUES GLU 1E, GLU1F, AND ARG 221A WERE NOT VISIBLE BEYOND CB. THEREFORE THE OCCUPANCY OF THESE ATOMS WERE SET TO 0. THE CONFORMATION OF THESE SIDE CHAINS WERE TAKEN FROM ANOTHER CRYSTAL FORM OF ETA (MONOCLINIC FORM). GLY 300: GLYCINE WAS MODELED INTO TO A STRONG FO-FC FEATURE DUE TO THE SHAPE AND ENVIRONMENT OF THE FEATURE.
RfactorNum. reflection% reflection
Rfree0.204 -10 %
Rwork0.172 --
obs0.172 16869 87.7 %
Refinement stepCycle: LAST / Resolution: 2.1→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 0 107 1990
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.498
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.09
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
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.09

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