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- PDB-5c2z: Molecular insights into the specificity of exfoliative toxins fro... -

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Basic information

Entry
Database: PDB / ID: 5c2z
TitleMolecular insights into the specificity of exfoliative toxins from Staphylococcus aureus
ComponentsExfoliative toxin D2
KeywordsTOXIN / esfoliative toxin / Staphylococcus aureus / ETD
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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.9553 Å
AuthorsMariutti, R.B. / Souza, T.A.C.B. / Ullah, A. / Zanphorlin, L.M. / Murakami, M.T. / Arni, R.K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Crystal structure of Staphylococcus aureus exfoliative toxin D-like protein: Structural basis for the high specificity of exfoliative toxins.
Authors: Mariutti, R.B. / Souza, T.A. / Ullah, A. / Caruso, I.P. / de Moraes, F.R. / Zanphorlin, L.M. / Tartaglia, N.R. / Seyffert, N. / Azevedo, V.A. / Le Loir, Y. / Murakami, M.T. / Arni, R.K.
History
DepositionJun 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence ...citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 6, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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 D2
B: Exfoliative toxin D2


Theoretical massNumber of molelcules
Total (without water)56,2992
Polymers56,2992
Non-polymers00
Water6,557364
1
A: Exfoliative toxin D2


Theoretical massNumber of molelcules
Total (without water)28,1501
Polymers28,1501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Exfoliative toxin D2


Theoretical massNumber of molelcules
Total (without water)28,1501
Polymers28,1501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.412, 93.141, 50.478
Angle α, β, γ (deg.)90.00, 91.23, 90.00
Int Tables number4
Space group name H-MP1211
DetailsMonomer confirmed by analytical ultracentrifugation

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Components

#1: Protein Exfoliative toxin D2


Mass: 28149.506 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: etD2 / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3) pLysS / References: UniProt: L0RUV7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.06 Å3/Da / Density % sol: 40.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5 / Details: 100 mM HEPES pH 7.5 30% 2-Propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 1.95→35.7 Å / Num. obs: 31792 / % possible obs: 96 % / Redundancy: 3.1 % / Net I/σ(I): 6.85

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9553→35.687 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2525 1616 5.08 %
Rwork0.1771 --
obs0.1809 31781 96.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9553→35.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3841 0 0 364 4205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073924
X-RAY DIFFRACTIONf_angle_d1.0715309
X-RAY DIFFRACTIONf_dihedral_angle_d13.6091457
X-RAY DIFFRACTIONf_chiral_restr0.042592
X-RAY DIFFRACTIONf_plane_restr0.004692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9553-2.01280.34861130.25222187X-RAY DIFFRACTION85
2.0128-2.07780.31370.22362398X-RAY DIFFRACTION92
2.0778-2.1520.30571610.20812488X-RAY DIFFRACTION97
2.152-2.23820.30361410.19722547X-RAY DIFFRACTION98
2.2382-2.340.28621270.19342546X-RAY DIFFRACTION97
2.34-2.46340.31491300.19292540X-RAY DIFFRACTION97
2.4634-2.61770.27381290.19082555X-RAY DIFFRACTION98
2.6177-2.81970.26721260.1882583X-RAY DIFFRACTION98
2.8197-3.10330.26811500.18352566X-RAY DIFFRACTION98
3.1033-3.5520.2381330.16942575X-RAY DIFFRACTION98
3.552-4.47380.2091270.14672577X-RAY DIFFRACTION98
4.4738-35.69260.20741420.15982603X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8125-1.5580.03163.6519-0.46440.40840.5180.1284-0.2683-0.1422-0.4409-0.5347-00.0686-0.04540.31180.0336-0.12320.35290.00220.51411.0553-16.8989-12.5657
23.44480.42030.12663.80792.0975.7272-0.14010.10750.2159-0.10650.2009-0.5224-0.28080.32560.02760.1979-0.00960.05220.1279-0.00530.24486.6541-15.1726-34.8077
33.1862-0.93020.2143.48880.79882.23820.0402-0.2946-0.02510.0272-0.10080.3195-0.1809-0.6202-0.04990.19570.034-0.01460.28540.0080.1672-12.2889-22.4794-31.1558
42.7299-1.16980.27751.64310.43332.04910.02320.09590.0878-0.3746-0.00160.0438-0.0875-0.346-0.02750.17920.0294-0.03310.23950.00220.1443-11.4142-18.0951-39.9907
51.64030.39920.70042.24750.5452.7369-0.0074-0.18830.0241-0.0148-0.0316-0.1738-0.0158-0.24090.03240.14470.03540.01860.1701-0.00060.1878-1.3822-24.7292-27.7077
64.77220.7552-0.00513.91-1.23022.7613-0.2246-0.0865-0.2147-0.190.00710.16170.9633-0.49050.17390.3136-0.06380.03990.24720.00870.2156-8.1962-40.4446-26.0912
72.4189-0.8728-1.95311.04210.38931.87560.214-0.11770.4470.0611-0.0101-0.1128-0.165-0.0718-0.14170.22920.00730.01110.1944-0.00890.2374-22.87656.36090.7241
82.62310.1809-0.67061.52270.03910.78550.18580.245-0.0738-0.2657-0.0842-0.0216-0.0792-0.0799-0.08150.21930.0570.00170.17420.020.1577-14.6561-1.4468-15.412
93.2142-1.5365-1.03641.73930.42111.74860.0853-0.14870.18260.04130.0123-0.1041-0.0327-0.1207-0.05550.1741-0.0166-0.00610.1761-0.00570.1485-23.0119-0.87370.1359
103.38480.3622-0.77672.60580.56332.33080.409-0.072-0.7301-0.1803-0.23550.12970.1993-0.1696-0.02660.3055-0.0003-0.11090.16450.02440.3275-21.8611-18.3142-9.6217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 66 )
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 104 )
4X-RAY DIFFRACTION4chain 'A' and (resid 105 through 136 )
5X-RAY DIFFRACTION5chain 'A' and (resid 137 through 248 )
6X-RAY DIFFRACTION6chain 'A' and (resid 249 through 278 )
7X-RAY DIFFRACTION7chain 'B' and (resid 32 through 84 )
8X-RAY DIFFRACTION8chain 'B' and (resid 85 through 159 )
9X-RAY DIFFRACTION9chain 'B' and (resid 160 through 248 )
10X-RAY DIFFRACTION10chain 'B' and (resid 249 through 279 )

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