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- PDB-9j9a: Staphylococcus aureus exfoliative toxin D -

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Basic information

Entry
Database: PDB / ID: 9j9a
TitleStaphylococcus aureus exfoliative toxin D
ComponentsSerine protease
KeywordsHYDROLASE / Serine protease / Desmoglein 1 / Staphylococcal scalded skin syndrome
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / 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
beta-D-glucopyranose / Serine protease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsTonozuka, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22H02515 Japan
Japan Society for the Promotion of Science (JSPS)23K23780 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Crystal structure of exfoliative toxin D from Staphylococcus aureus.
Authors: Sato, S. / Ragab, R.F. / Guo, X. / Elfadadny, A. / Kozono, T. / Nishikawa, A. / Nishifuji, K. / Tonozuka, T.
History
DepositionAug 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 25, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3486
Polymers28,6991
Non-polymers6495
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-31 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.597, 122.597, 60.514
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Serine protease


Mass: 28699.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The numbering of the amino acid residues begins with the N-terminus of the mature enzyme and does not include the signal sequence in GenBank BAC22944. Methionine is artificially placed at ...Details: The numbering of the amino acid residues begins with the N-terminus of the mature enzyme and does not include the signal sequence in GenBank BAC22944. Methionine is artificially placed at the N-terminus, and C-terminal tag sequence is HRSRSHHHHHH.
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: etd / Production host: Escherichia coli (E. coli)
References: UniProt: Q8GAX8, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: ammonium sulfate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→43.06 Å / Num. obs: 52340 / % possible obs: 99.8 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.014 / Net I/σ(I): 35.6
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2858 / Rpim(I) all: 0.253

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF-Q8GAX8-F1

Resolution: 1.75→43.06 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17962 2684 5.1 %RANDOM
Rwork0.1615 ---
obs0.16241 49640 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.164 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.75→43.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 0 39 156 2105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121987
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161864
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.6642684
X-RAY DIFFRACTIONr_angle_other_deg0.6431.5754338
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9175249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.20355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06410351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0570.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022237
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02415
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0543.186993
X-RAY DIFFRACTIONr_mcbond_other2.053.185993
X-RAY DIFFRACTIONr_mcangle_it3.2685.7071240
X-RAY DIFFRACTIONr_mcangle_other3.2675.7131241
X-RAY DIFFRACTIONr_scbond_it2.8483.696994
X-RAY DIFFRACTIONr_scbond_other2.8463.699995
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.686.5961444
X-RAY DIFFRACTIONr_long_range_B_refined6.28431.62202
X-RAY DIFFRACTIONr_long_range_B_other6.23431.042170
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 237 -
Rwork0.227 3596 -
obs--99.46 %

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