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- PDB-8t3j: Crystal structure of native exfoliative toxin C (ExhC) from Mamma... -

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Basic information

Entry
Database: PDB / ID: 8t3j
TitleCrystal structure of native 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: 2.705 Å
AuthorsCalil, F.A. / Gismene, C. / 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 1.1Feb 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)85,7603
Polymers85,7603
Non-polymers00
Water1,00956
1
A: Exfoliative toxin C


Theoretical massNumber of molelcules
Total (without water)28,5871
Polymers28,5871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exfoliative toxin C


Theoretical massNumber of molelcules
Total (without water)28,5871
Polymers28,5871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Exfoliative toxin C


Theoretical massNumber of molelcules
Total (without water)28,5871
Polymers28,5871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.094, 167.094, 157.743
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-322-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A

NCS domain segments:

Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A

Dom-IDComponent-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth seq-IDLabel seq-ID
111LEULEU5 - 2415 - 241
211LEULEU5 - 2415 - 241
322LEULEU5 - 2415 - 241
422LEULEU5 - 2415 - 241
533ILEILE5 - 2425 - 242
633ILEILE5 - 2425 - 242

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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Components

#1: Protein Exfoliative toxin C / Serine protease


Mass: 28586.680 Da / Num. of mol.: 3
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.: 56 / 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: 3.21 Å3/Da / Density % sol: 61.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5 and 0.8 M Potassium/Sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 3, 2021
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 2.705→47.283 Å / Num. obs: 30672 / % possible obs: 99.92 % / Redundancy: 26.2 % / CC1/2: 0.995 / CC star: 0.999 / Rpim(I) all: 0.06747 / Net I/σ(I): 8.4
Reflection shellResolution: 2.71→2.807 Å / Mean I/σ(I) obs: 0.79 / Num. unique obs: 3017 / CC1/2: 0.45 / Rpim(I) all: 0.7518

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.705→47.283 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.256 / WRfactor Rwork: 0.198 / SU B: 33.546 / SU ML: 0.296 / Average fsc free: 0.9408 / Average fsc work: 0.9533 / Cross valid method: FREE R-VALUE / ESU R: 0.522 / ESU R Free: 0.325
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2701 1534 5.001 %
Rwork0.2113 29138 -
all0.214 --
obs-30672 99.808 %
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: 80.759 Å2
Baniso -1Baniso -2Baniso -3
1--1.437 Å20 Å2-0 Å2
2---1.437 Å2-0 Å2
3---2.875 Å2
Refinement stepCycle: LAST / Resolution: 2.705→47.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5502 0 0 56 5558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125622
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165200
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.6447601
X-RAY DIFFRACTIONr_angle_other_deg0.5171.58412014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.835713
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.786515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.19810933
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.2410262
X-RAY DIFFRACTIONr_chiral_restr0.0670.2818
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026611
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021273
X-RAY DIFFRACTIONr_nbd_refined0.2180.21257
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.25355
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22797
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.23100
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2127
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1290.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1650.212
X-RAY DIFFRACTIONr_nbd_other0.1930.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2610.28
X-RAY DIFFRACTIONr_mcbond_it6.1176.082861
X-RAY DIFFRACTIONr_mcbond_other6.1176.082861
X-RAY DIFFRACTIONr_mcangle_it9.210.9293571
X-RAY DIFFRACTIONr_mcangle_other9.210.9313572
X-RAY DIFFRACTIONr_scbond_it6.6316.3852761
X-RAY DIFFRACTIONr_scbond_other6.6296.3852762
X-RAY DIFFRACTIONr_scangle_it10.05811.5314030
X-RAY DIFFRACTIONr_scangle_other10.05611.534031
X-RAY DIFFRACTIONr_lrange_it13.18457.5186217
X-RAY DIFFRACTIONr_lrange_other13.18657.5196213
X-RAY DIFFRACTIONr_ncsr_local_group_10.0950.057523
X-RAY DIFFRACTIONr_ncsr_local_group_20.1060.057352
X-RAY DIFFRACTIONr_ncsr_local_group_30.0970.057586
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.09540.0501
12AX-RAY DIFFRACTIONLocal ncs0.09540.0501
23AX-RAY DIFFRACTIONLocal ncs0.106320.05009
24AX-RAY DIFFRACTIONLocal ncs0.106320.05009
35AX-RAY DIFFRACTIONLocal ncs0.096730.0501
36AX-RAY DIFFRACTIONLocal ncs0.096730.0501
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
2.705-2.7750.5931090.54320690.54522260.8670.87197.84370.541
2.775-2.8510.4451090.46420650.46321740.9060.8831000.46
2.851-2.9330.4451050.41620130.41721180.9210.9041000.416
2.933-3.0230.361040.30519660.30820700.9220.941000.301
3.023-3.1220.313980.24318710.24619690.9220.9571000.229
3.122-3.2310.367980.24218590.24819570.9150.9581000.223
3.231-3.3520.243930.21717520.21818450.9570.9681000.198
3.352-3.4890.246910.20317390.20518300.9660.9791000.187
3.489-3.6430.246870.18216430.18517300.9590.9821000.166
3.643-3.8190.233820.17115720.17416540.9660.9831000.158
3.819-4.0250.249790.18614970.18915760.9540.9771000.172
4.025-4.2670.205750.1714330.17215080.9720.981000.16
4.267-4.5590.251710.15713460.16114170.9620.9841000.152
4.559-4.920.167670.14312650.14413320.9840.9861000.141
4.92-5.3840.252600.16411500.16912100.9620.9831000.159
5.384-6.010.224570.15810710.16111280.9730.9851000.154
6.01-6.9210.32490.2299450.2349940.9540.9711000.225
6.921-8.4310.276440.2658170.2668610.9580.9641000.264
8.431-11.7380.292340.2076490.2126830.9580.9761000.229
11.738-47.2830.352220.324160.3224380.9410.9391000.337
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)
11.83210.9291-0.40025.97290.57571.2782-0.04640.0948-0.4669-0.2350.0525-0.7470.20030.1446-0.00610.05410.0310.02410.03-0.03010.1675-26.511412.3737-47.623
21.79230.2332-0.89621.24360.32845.6059-0.0440.4953-0.1103-0.2333-0.02930.17510.1826-0.68450.07320.0557-0.0142-0.03540.1766-0.0410.0369-57.060235.9888-66.6279
31.4625-0.6573-0.25816.0603-1.36352.1414-0.0762-0.13830.26270.86550.19960.3135-0.5932-0.2746-0.12340.2140.08750.04080.0569-0.01970.0802-47.6682-12.2728-26.7171
Refinement TLS groupSelection: ALL

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