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- PDB-1due: CRYSTAL STRUCTURE OF EXFOLIATIVE TOXIN A S195A MUTANT -

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Basic information

Entry
Database: PDB / ID: 1due
TitleCRYSTAL STRUCTURE OF EXFOLIATIVE TOXIN A S195A MUTANT
ComponentsEXFOLIATIVE TOXIN A
KeywordsTOXIN / HYDROLASE / superantigens / protease / epidermis
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
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsPapageorgiou, A.C. / Plano, L.R.W. / Collins, C.M. / Acharya, K.R.
CitationJournal: Protein Sci. / Year: 2000
Title: Structural similarities and differences in Staphylococcus aureus exfoliative Toxins A and B as revealed by their crystal structures
Authors: Papageorgiou, A.C. / Plano, L.R. / Collins, C.M. / Acharya, K.R.
History
DepositionJan 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EXFOLIATIVE TOXIN A


Theoretical massNumber of molelcules
Total (without water)26,9691
Polymers26,9691
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.002, 67.366, 48.076
Angle α, β, γ (deg.)90.00, 118.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein EXFOLIATIVE TOXIN A


Mass: 26969.109 Da / Num. of mol.: 1 / Mutation: S195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Description: CHROMOSOMAL DNA OF S. AUREUS ISOLATED FROM A PATIENT WITH STAPHYLOCOCCAL SCALDED SKIN DISEASE
Plasmid: PET15B / Production host: Escherichia coli (E. coli)
References: UniProt: P09331, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, Ammonium sulphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
23.5 Msodium formate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12891
22891
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONEMBL/DESY, HAMBURG X3110.837
SYNCHROTRONSRS PX9.620.96
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEJan 15, 1998
ADSC2CCDJan 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.8371
20.961
ReflectionResolution: 2→40 Å / Num. all: 17178 / Num. obs: 17178 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 40.4 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 11
Reflection shellResolution: 2→2.1 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.46 / % possible all: 97.1
Reflection
*PLUS
Lowest resolution: 40 Å / % possible obs: 94 % / Num. measured all: 120003
Reflection shell
*PLUS
% possible obs: 97.1 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflectionSelection details
Rfree0.238 826 5%
Rwork0.214 --
all0.214 17178 -
obs0.214 16890 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 0 41 1945
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.22
X-RAY DIFFRACTIONc_torsion_deg25.5
X-RAY DIFFRACTIONc_torsion_impr_deg0.94
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73

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