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- PDB-8dax: New insights into the P186 flip and oligomeric state of Staphyloc... -

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Basic information

Entry
Database: PDB / ID: 8dax
TitleNew insights into the P186 flip and oligomeric state of Staphylococcus aureus exfoliative toxin E: implications for the exfoliative mechanism
ComponentsExfoliative toxin E
KeywordsTOXIN / ETE
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 / 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: 1.61 Å
AuthorsGismene, C. / Nascimento, A.F.Z. / Hernandez-Gonzalez, J.E. / Santisteban, A.R.N. / de Moraes, F.R. / Arni, R.K. / Mariutti, R.B.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2020/13921-0 Brazil
Sao Paulo Research Foundation (FAPESP)2021/10214-1 Brazil
Sao Paulo Research Foundation (FAPESP)2018/07977-3 Brazil
CitationJournal: Int J Mol Sci / Year: 2022
Title: Staphylococcus aureus Exfoliative Toxin E, Oligomeric State and Flip of P186: Implications for Its Action Mechanism.
Authors: Gismene, C. / Hernandez Gonzalez, J.E. / Santisteban, A.R.N. / Ziem Nascimento, A.F. / Dos Santos Cunha, L. / de Moraes, F.R. / de Oliveira, C.L.P. / Oliveira, C.C. / Jocelan Scarin ...Authors: Gismene, C. / Hernandez Gonzalez, J.E. / Santisteban, A.R.N. / Ziem Nascimento, A.F. / Dos Santos Cunha, L. / de Moraes, F.R. / de Oliveira, C.L.P. / Oliveira, C.C. / Jocelan Scarin Provazzi, P. / Pascutti, P.G. / Arni, R.K. / Barros Mariutti, R.
History
DepositionJun 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,0242
Polymers57,0242
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.744, 97.744, 116.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Exfoliative toxin E / Serine protease


Mass: 28511.910 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)
References: UniProt: L0RUV7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 4 M Sodium Formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4587 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 23, 2019
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4587 Å / Relative weight: 1
ReflectionResolution: 1.61→48.92 Å / Num. obs: 138763 / % possible obs: 100 % / Redundancy: 13.314 % / Biso Wilson estimate: 36.271 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.078 / Χ2: 1.09 / Net I/σ(I): 17.85 / Num. measured all: 1847423
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.61-1.7112.742.3220.9528607222480224540.4552.41999.9
1.71-1.8312.4481.1941.9426201621050210490.7531.246100
1.83-1.9813.7070.5344.6826975319680196800.9410.554100
1.98-2.1613.6330.2569.6824601518045180450.9860.266100
2.16-2.4212.6840.14116.620686216309163090.9950.146100
2.42-2.7914.3210.08727.8120650914420144200.9980.09100
2.79-3.4214.0180.05544.7617066712175121750.9990.057100
3.42-4.8212.9140.04160.62121586941594150.9990.043100
4.82-48.9214.9430.03969.1577943522652160.9990.04199.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C2Z

5c2z


Resolution: 1.61→48.92 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.514 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2479 3650 5 %RANDOM
Rwork0.2142 ---
obs0.2158 69347 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.75 Å2 / Biso mean: 33.64 Å2 / Biso min: 16.84 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.61→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3838 0 0 145 3983
Biso mean---34.42 -
Num. residues----496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133937
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173632
X-RAY DIFFRACTIONr_angle_refined_deg1.7761.6535326
X-RAY DIFFRACTIONr_angle_other_deg1.4181.5798496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8445498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09824.13184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36115685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2721513
X-RAY DIFFRACTIONr_chiral_restr0.0820.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024403
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02772
LS refinement shellResolution: 1.614→1.656 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 266 -
Rwork0.353 5058 -
all-5324 -
obs--99.64 %

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