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- PDB-9bsh: Staphylococcus aureus exfoliative toxin A D164A variant -

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Basic information

Entry
Database: PDB / ID: 9bsh
TitleStaphylococcus aureus exfoliative toxin A D164A variant
ComponentsExfoliative toxin A
KeywordsTOXIN / exfoliative toxin
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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsHolyoak, T. / Tran, N.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Sci Adv / Year: 2025
Title: Identifying and controlling inactive and active conformations of a serine protease.
Authors: Lee, E. / Tran, N. / Redzic, J.S. / Singh, H. / Alamillo, L. / Holyoak, T. / Hamelberg, D. / Eisenmesser, E.Z.
History
DepositionMay 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exfoliative toxin A
B: Exfoliative toxin A


Theoretical massNumber of molelcules
Total (without water)62,1822
Polymers62,1822
Non-polymers00
Water16,340907
1
A: Exfoliative toxin A


Theoretical massNumber of molelcules
Total (without water)31,0911
Polymers31,0911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exfoliative toxin A


Theoretical massNumber of molelcules
Total (without water)31,0911
Polymers31,0911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.551, 66.543, 81.810
Angle α, β, γ (deg.)90.00, 94.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Exfoliative toxin A / Epidermolytic toxin A


Mass: 31091.061 Da / Num. of mol.: 2 / Mutation: D202A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: eta / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P09331, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 907 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.12 Å3/Da / Density % sol: 41.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M magnesium formate, 17.5% PEG 3350 (MCSG1 G10), 2:2 uL protein:mother liquor with a protein concentration of 17.5 mg/mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18069 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18069 Å / Relative weight: 1
ReflectionResolution: 1.35→66.62 Å / Num. obs: 109787 / % possible obs: 96.38 % / Redundancy: 6.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.037 / Rrim(I) all: 0.088 / Net I/σ(I): 21.8
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 6.5 / Num. unique obs: 5330 / CC1/2: 0.675 / Rpim(I) all: 0.16 / Rrim(I) all: 0.381 / % possible all: 95.3

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Processing

Software
NameVersionClassification
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
PHENIX(1.20.1_4487: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→51.57 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2271 5555 5.06 %
Rwork0.199 --
obs0.2003 109726 96.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→51.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3814 0 0 907 4721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063999
X-RAY DIFFRACTIONf_angle_d0.9585420
X-RAY DIFFRACTIONf_dihedral_angle_d5.742559
X-RAY DIFFRACTIONf_chiral_restr0.09583
X-RAY DIFFRACTIONf_plane_restr0.007719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.360.30111910.27813259X-RAY DIFFRACTION93
1.36-1.380.2881790.2743439X-RAY DIFFRACTION96
1.38-1.40.27021900.27253428X-RAY DIFFRACTION96
1.4-1.420.2762060.26143431X-RAY DIFFRACTION95
1.42-1.430.28691520.25573487X-RAY DIFFRACTION96
1.43-1.450.30421890.2513411X-RAY DIFFRACTION96
1.45-1.470.2852000.25183508X-RAY DIFFRACTION96
1.47-1.50.28671980.24693419X-RAY DIFFRACTION96
1.5-1.520.28011830.23893446X-RAY DIFFRACTION96
1.52-1.540.2981690.23153450X-RAY DIFFRACTION96
1.54-1.570.25822030.23473452X-RAY DIFFRACTION96
1.57-1.60.25831800.23293412X-RAY DIFFRACTION96
1.6-1.630.22491830.22893434X-RAY DIFFRACTION95
1.63-1.660.25972010.24253410X-RAY DIFFRACTION95
1.66-1.70.2591900.23493449X-RAY DIFFRACTION96
1.7-1.740.23841680.23153505X-RAY DIFFRACTION96
1.74-1.780.24292100.22263395X-RAY DIFFRACTION95
1.78-1.830.2511720.21663423X-RAY DIFFRACTION96
1.83-1.890.24981730.21923440X-RAY DIFFRACTION95
1.89-1.950.25691750.2183554X-RAY DIFFRACTION98
1.95-2.020.24512140.21293483X-RAY DIFFRACTION97
2.02-2.10.23831920.21363547X-RAY DIFFRACTION98
2.1-2.190.20991890.20253471X-RAY DIFFRACTION97
2.19-2.310.22481690.19653498X-RAY DIFFRACTION96
2.31-2.450.22691780.19183463X-RAY DIFFRACTION96
2.45-2.640.2172010.18743480X-RAY DIFFRACTION97
2.64-2.910.20661840.18083530X-RAY DIFFRACTION98
2.91-3.330.21331870.15963584X-RAY DIFFRACTION98
3.33-4.190.17521800.14893630X-RAY DIFFRACTION99
4.19-51.570.16041490.16133755X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 12.9634 Å / Origin y: -17.201 Å / Origin z: 20.5404 Å
111213212223313233
T0.0573 Å2-0.0244 Å2-0.0053 Å2-0.061 Å2-0.0021 Å2--0.0463 Å2
L0.1873 °2-0.1762 °2-0.0464 °2-0.2107 °20.0171 °2--0.0221 °2
S-0.0095 Å °0.0088 Å °0.0006 Å °0.0111 Å °0.0088 Å °-0.0027 Å °0.0064 Å °-0.001 Å °0.0162 Å °
Refinement TLS groupSelection details: all

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