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- PDB-9bsm: Staphylococcus aureus exfoliative toxin A D164E variant -

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Basic information

Entry
Database: PDB / ID: 9bsm
TitleStaphylococcus aureus exfoliative toxin A D164E variant
ComponentsExfoliative toxin A
KeywordsTOXIN / exfoliative toxin
Function / homology
Function and homology information


symbiont-mediated disruption of host cell-cell adhesion / 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: 1.48 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


Theoretical massNumber of molelcules
Total (without water)31,1491
Polymers31,1491
Non-polymers00
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.380, 66.392, 48.295
Angle α, β, γ (deg.)90.00, 116.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Exfoliative toxin A / Epidermolytic toxin A


Mass: 31149.092 Da / Num. of mol.: 1 / Mutation: D202E
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.: 193 / 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: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50mM sodium phosphate, pH 7.0, 22.5% PEG 4000, 2:2 uL protein:mother liquor, protein concentration 15 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: 1.48→43.08 Å / Num. obs: 42293 / % possible obs: 99 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.035 / Rrim(I) all: 0.091 / Net I/σ(I): 14.5
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2063 / CC1/2: 0.636 / Rpim(I) all: 0.346 / Rrim(I) all: 0.842 / % possible all: 97.4

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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: 1.48→40.44 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2205 2009 4.77 %
Rwork0.1939 --
obs0.1951 42123 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.48→40.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1870 0 0 193 2063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061918
X-RAY DIFFRACTIONf_angle_d0.8732591
X-RAY DIFFRACTIONf_dihedral_angle_d5.633261
X-RAY DIFFRACTIONf_chiral_restr0.078277
X-RAY DIFFRACTIONf_plane_restr0.007343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.520.36971260.38772792X-RAY DIFFRACTION96
1.52-1.560.37261410.35732787X-RAY DIFFRACTION97
1.56-1.60.31941540.32422821X-RAY DIFFRACTION98
1.6-1.650.3181330.29632848X-RAY DIFFRACTION98
1.65-1.710.26451690.2552798X-RAY DIFFRACTION98
1.71-1.780.23491600.23482843X-RAY DIFFRACTION99
1.78-1.860.26651360.22242887X-RAY DIFFRACTION99
1.86-1.960.2051430.20072897X-RAY DIFFRACTION99
1.96-2.080.20161310.19222882X-RAY DIFFRACTION100
2.08-2.240.20851520.19062884X-RAY DIFFRACTION100
2.24-2.470.22971800.18932852X-RAY DIFFRACTION99
2.47-2.830.22371380.17862891X-RAY DIFFRACTION99
2.83-3.560.22161120.16912940X-RAY DIFFRACTION100
3.56-40.440.16571340.15382992X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 14.7014 Å / Origin y: 0.0847 Å / Origin z: 8.4411 Å
111213212223313233
T0.1209 Å2-0.0447 Å2-0.0457 Å2-0.1612 Å20.0421 Å2--0.1211 Å2
L1.8054 °2-1.0606 °2-0.2355 °2-5.901 °2-0.3468 °2--2.5115 °2
S-0.0194 Å °-0.1111 Å °-0.1556 Å °-0.507 Å °0.1934 Å °0.4818 Å °-0.0218 Å °-0.2802 Å °-0.0557 Å °
Refinement TLS groupSelection details: all

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