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- PDB-1dt2: CRYSTAL STRUCTURE OF EXFOLIATIVE TOXIN B -

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Basic information

Entry
Database: PDB / ID: 1dt2
TitleCRYSTAL STRUCTURE OF EXFOLIATIVE TOXIN B
ComponentsEXFOLIATIVE TOXIN B
Keywordstoxin / hydrolase / epidermolysis / superantigen / serine protease
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 / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H ...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 / Serine proteases, trypsin domain / Trypsin / 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: 2.8 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 11, 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 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EXFOLIATIVE TOXIN B


Theoretical massNumber of molelcules
Total (without water)27,2191
Polymers27,2191
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.248, 114.248, 96.477
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-255-

HOH

DetailsThe biological assembly is a monomer

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Components

#1: Protein EXFOLIATIVE TOXIN B


Mass: 27219.371 Da / Num. of mol.: 1
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: P09332, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 1

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Sample preparation

Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: NaFormate-no pH adjusted, so the pH should be around 8.0, 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9057
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 4, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9057 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 15313 / Num. obs: 13063 / % possible obs: 85.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 73.9 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.2
Reflection shellResolution: 2.8→20 Å / Redundancy: 8 % / Rmerge(I) obs: 0.423 / % possible all: 69.3
Reflection
*PLUS
% possible obs: 85 % / Num. measured all: 66486
Reflection shell
*PLUS
Lowest resolution: 2.9 Å / % possible obs: 69 % / Mean I/σ(I) obs: 2.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2.8→20 Å / σ(F): 0 / σ(I): -3
RfactorNum. reflectionSelection details
Rfree0.251 669 4.4% of the reflections
Rwork0.224 --
obs-13063 -
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1899 0 0 9 1908
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.58
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_torsion_deg25.41
X-RAY DIFFRACTIONx_torsion_impr_deg1.02
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rwork: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.45
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.29
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.87

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