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- PDB-8t3i: Crystal structure of mutant exfoliative toxin C (ExhC) from Mamma... -

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Basic information

Entry
Database: PDB / ID: 8t3i
TitleCrystal structure of mutant exfoliative toxin C (ExhC) from Mammaliicoccus sciuri
ComponentsExfoliative toxin C
KeywordsTOXIN / peptidase / necrotic activity
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
Biological speciesMammaliicoccus sciuri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsGismene, C. / Calil, F.A. / Hernandez Gonzalez, J.E. / Ziem Nascimento, A.F. / Santisteban, A.R.N. / Arni, R.K. / Barros Mariutti, R.
Funding support Brazil, 4items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2020/08165-8 Brazil
Sao Paulo Research Foundation (FAPESP)2020/13921-0 Brazil
Sao Paulo Research Foundation (FAPESP)2022/14362-0 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Necrotic activity of ExhC from Mammaliicoccus sciuri is mediated by specific amino acid residues.
Authors: Gismene, C. / Gonzalez, J.E.H. / de Freitas Calmon, M. / Nascimento, A.F.Z. / Santisteban, A.R.N. / Calil, F.A. / da Silva, A.D.T. / Rahal, P. / Goes, R.M. / Arni, R.K. / Mariutti, R.B.
History
DepositionJun 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID / _audit_author.name
Revision 1.2Feb 14, 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 / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,8972
Polymers56,8972
Non-polymers00
Water5,098283
1
A: Exfoliative toxin C


Theoretical massNumber of molelcules
Total (without water)28,4491
Polymers28,4491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exfoliative toxin C


Theoretical massNumber of molelcules
Total (without water)28,4491
Polymers28,4491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.150, 71.398, 71.383
Angle α, β, γ (deg.)90.000, 94.705, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Exfoliative toxin C / Serine protease


Mass: 28448.574 Da / Num. of mol.: 2 / Mutation: R47A, N49F, Q51K, R89A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammaliicoccus sciuri (bacteria) / Gene: exhC / Production host: Escherichia coli (E. coli) / References: UniProt: F6M8N2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.02 Å3/Da / Density % sol: 38.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M MgCl2; 0.1 M Tris-HCl pH 8.5 and 30% w/v PEG 4000 with the addition of 0.1 M Sarcosine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 1.32363 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 14, 2020
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.32363 Å / Relative weight: 1
ReflectionResolution: 1.57→39.553 Å / Num. obs: 63061 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06174 / Rpim(I) all: 0.02589 / Net I/σ(I): 15.17
Reflection shellResolution: 1.57→1.626 Å / Rmerge(I) obs: 0.06174 / Mean I/σ(I) obs: 1.14 / Num. unique obs: 6315 / CC1/2: 0.506 / Rpim(I) all: 0.5632

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→39.553 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.248 / SU ML: 0.076 / Cross valid method: FREE R-VALUE / ESU R: 0.087 / ESU R Free: 0.092
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2229 3153 5 %
Rwork0.1813 59908 -
all0.183 --
obs-63061 99.894 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.023 Å2
Baniso -1Baniso -2Baniso -3
1--1.512 Å20 Å20.232 Å2
2--1.167 Å2-0 Å2
3---0.303 Å2
Refinement stepCycle: LAST / Resolution: 1.57→39.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3711 0 0 283 3994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0123787
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163506
X-RAY DIFFRACTIONr_angle_refined_deg2.1521.6415120
X-RAY DIFFRACTIONr_angle_other_deg0.6991.5838116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1585478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.90456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36210630
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.77910176
X-RAY DIFFRACTIONr_chiral_restr0.1070.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.024414
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02846
X-RAY DIFFRACTIONr_nbd_refined0.2130.2706
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.23236
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21906
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.22059
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2191
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0080.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.120.27
X-RAY DIFFRACTIONr_nbd_other0.1370.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2120.222
X-RAY DIFFRACTIONr_mcbond_it3.3362.5591918
X-RAY DIFFRACTIONr_mcbond_other3.3362.5581918
X-RAY DIFFRACTIONr_mcangle_it4.354.5892394
X-RAY DIFFRACTIONr_mcangle_other4.3514.5912395
X-RAY DIFFRACTIONr_scbond_it5.1243.0661869
X-RAY DIFFRACTIONr_scbond_other5.1233.0681870
X-RAY DIFFRACTIONr_scangle_it7.4155.3412726
X-RAY DIFFRACTIONr_scangle_other7.4135.3432727
X-RAY DIFFRACTIONr_lrange_it8.37827.5354212
X-RAY DIFFRACTIONr_lrange_other8.38526.8534152
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.57-1.610.3562310.3443940.34146670.910.9299.10010.34
1.61-1.6540.3162260.29543040.29645300.9280.9421000.294
1.654-1.7020.3342180.26441390.26743590.9330.95499.95410.256
1.702-1.7550.2542140.22240700.22442840.9610.9681000.206
1.755-1.8120.2442070.19939310.20141380.9560.9741000.179
1.812-1.8760.272020.20138430.20540450.9540.9741000.18
1.876-1.9460.281940.22836700.23138640.9520.9671000.204
1.946-2.0250.2451850.19635240.19937090.960.9761000.175
2.025-2.1150.2631800.19934170.20235970.9570.9761000.18
2.115-2.2180.2181710.18532580.18734290.9720.9791000.169
2.218-2.3380.2331620.18530720.18732360.9680.9899.93820.165
2.338-2.4790.2221540.1729210.17330760.9710.98399.96750.159
2.479-2.6490.2241470.16727930.1729400.9690.9831000.158
2.649-2.8610.2151340.17925550.18126890.9710.981000.173
2.861-3.1320.2111250.17923730.18125000.9760.98199.920.18
3.132-3.4990.241130.18321350.18622530.9640.9899.77810.192
3.499-4.0350.1871000.15419020.15620120.9810.98799.5030.167
4.035-4.9290.138840.12416070.12516910.9890.9921000.146
4.929-6.9170.208670.17112590.17313260.9880.9881000.191
6.917-39.5530.205390.1717410.1737800.9740.9831000.203

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