[English] 日本語
Yorodumi
- PDB-8t3i: Crystal structure of mutant exfoliative toxin C (ExhC) from Mamma... -

+
Open data


ID or keywords:

Loading...

-
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 / extracellular region
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more