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

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Basic information

Entry
Database: PDB / ID: 1qtf
TitleCRYSTAL STRUCTURE OF EXFOLIATIVE TOXIN B
ComponentsEXFOLIATIVE TOXIN B
KeywordsHYDROLASE / TOXIN / SERINE PROTEASE / SUPERANTIGEN
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 / Resolution: 2.4 Å
AuthorsVath, G.M. / Earhart, C.A. / Monie, D.D. / Schlievert, P.M. / Ohlendorf, D.H.
CitationJournal: Biochemistry / Year: 1999
Title: The crystal structure of exfoliative toxin B: a superantigen with enzymatic activity.
Authors: Vath, G.M. / Earhart, C.A. / Monie, D.D. / Iandolo, J.J. / Schlievert, P.M. / Ohlendorf, D.H.
History
DepositionJun 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)27,2921
Polymers27,2921
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.97, 71.09, 108.37
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: Protein EXFOLIATIVE TOXIN B / E.C.3.4.21.- / EPIDERMOLYTIC TOXIN B


Mass: 27291.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Plasmid: PRW001 / Strain: RN4220
References: UniProt: P09332, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: HEPES, MPD, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / PH range low: 7.5 / PH range high: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
225-30 %MPD1reservoir
350 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Dec 16, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. all: 10085 / Num. obs: 10085 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 10.1
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.33 / % possible all: 52
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 52 % / Mean I/σ(I) obs: 1.03

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
X-GENdata reduction
X-GENdata scaling
X-PLORphasing
RefinementResolution: 2.4→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.29 667 7 %random
Rwork0.204 ---
all-10085 --
obs-10085 8 %-
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 0 12 1935
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 7 % / Rfactor obs: 0.204 / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.7
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.5 Å / Rfactor Rfree: 0.45 / Rfactor obs: 0.33

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