[English] 日本語
Yorodumi
- PDB-6t1c: Structure of the C7S mutant of mosquitocidal Cyt1A protoxin obtai... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6t1c
TitleStructure of the C7S mutant of mosquitocidal Cyt1A protoxin obtained by Serial Femtosecond Crystallography on in vivo grown crystals at pH 7
ComponentsType-1Aa cytolytic delta-endotoxin
KeywordsTOXIN / Mosquitocidal toxin / in vivo grown nanocrystals
Function / homologyDelta-endotoxin CytB / Delta-endotoxin CytB-like superfamily / Bacillus thuringiensis toxin / sporulation resulting in formation of a cellular spore / toxin activity / extracellular region / Type-1Aa cytolytic delta-endotoxin
Function and homology information
Biological speciesBacillus thuringiensis subsp. israelensis (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTetreau, G. / Banneville, A.S. / Andreeva, E. / Brewster, A.S. / Hunter, M.S. / Sierra, R.G. / Young, I.D. / Boutet, S. / Coquelle, N. / Cascio, D. ...Tetreau, G. / Banneville, A.S. / Andreeva, E. / Brewster, A.S. / Hunter, M.S. / Sierra, R.G. / Young, I.D. / Boutet, S. / Coquelle, N. / Cascio, D. / Sawaya, M.R. / Sauter, N.K. / Colletier, J.P.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-17-CE11-0018-01 France
French National Research AgencyANR-2018-CE11-0005-02 France
CitationJournal: Nat Commun / Year: 2020
Title: Serial femtosecond crystallography on in vivo-grown crystals drives elucidation of mosquitocidal Cyt1Aa bioactivation cascade.
Authors: Tetreau, G. / Banneville, A.S. / Andreeva, E.A. / Brewster, A.S. / Hunter, M.S. / Sierra, R.G. / Teulon, J.M. / Young, I.D. / Burke, N. / Grunewald, T.A. / Beaudouin, J. / Snigireva, I. / ...Authors: Tetreau, G. / Banneville, A.S. / Andreeva, E.A. / Brewster, A.S. / Hunter, M.S. / Sierra, R.G. / Teulon, J.M. / Young, I.D. / Burke, N. / Grunewald, T.A. / Beaudouin, J. / Snigireva, I. / Fernandez-Luna, M.T. / Burt, A. / Park, H.W. / Signor, L. / Bafna, J.A. / Sadir, R. / Fenel, D. / Boeri-Erba, E. / Bacia, M. / Zala, N. / Laporte, F. / Despres, L. / Weik, M. / Boutet, S. / Rosenthal, M. / Coquelle, N. / Burghammer, M. / Cascio, D. / Sawaya, M.R. / Winterhalter, M. / Gratton, E. / Gutsche, I. / Federici, B. / Pellequer, J.L. / Sauter, N.K. / Colletier, J.P.
History
DepositionOct 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
BBB: Type-1Aa cytolytic delta-endotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3622
Polymers27,3391
Non-polymers231
Water4,936274
1
BBB: Type-1Aa cytolytic delta-endotoxin
hetero molecules

BBB: Type-1Aa cytolytic delta-endotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7244
Polymers54,6782
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area6490 Å2
ΔGint-49 kcal/mol
Surface area21240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.666, 65.666, 164.066
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11BBB-635-

HOH

21BBB-673-

HOH

-
Components

#1: Protein Type-1Aa cytolytic delta-endotoxin / 27 kDa cytolytic toxin


Mass: 27338.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C7S mutant of Cyt1Aa
Source: (gene. exp.) Bacillus thuringiensis subsp. israelensis (bacteria)
Gene: cyt1Aa, cytA / Variant: C7S mutant
Production host: Bacillus thuringiensis serovar israelensis (bacteria)
Variant (production host): 4Q7 / References: UniProt: P0A382
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.51 % / Description: ball-like crystals.
Crystal growTemperature: 300 K / Method: in cell / pH: 7
Details: In cell crystallization by recombinant expression in a Bacillus thuringiensis serovar israelensis strain devoid of its pBt plasmid.

-
Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.28 Å
DetectorType: CS-PAD CXI-2 / Detector: PIXEL / Date: Nov 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 14420 / % possible obs: 99.9 % / Redundancy: 65.8 % / CC1/2: 0.994 / R split: 0.125 / Net I/σ(I): 19.8
Reflection shellResolution: 1.97→2.01 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 877 / CC1/2: 0.178 / R split: 0.616
Serial crystallography measurementFocal spot size: 1.7 µm2 / Pulse duration: 40 fsec. / Pulse energy: 1000 µJ / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionDescription: MESH
Serial crystallography data reductionFrames indexed: 7683 / Frames total: 18218 / Lattices indexed: 7754

-
Processing

Software
NameVersionClassification
REFMAC5.8.0230 2018/03/05refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6t14

6t14


Resolution: 2→14.838 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.195 / WRfactor Rwork: 0.143 / Cross valid method: FREE R-VALUE / ESU R: 0.295 / ESU R Free: 0.223
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2691 722 -
Rwork0.2116 13698 -
all0.214 --
obs-14420 96.681 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 35.915 Å2
Baniso -1Baniso -2Baniso -3
1--0.001 Å20 Å20 Å2
2---0.001 Å20 Å2
3---0.002 Å2
Refinement stepCycle: LAST / Resolution: 2→14.838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1882 0 1 276 2159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121981
X-RAY DIFFRACTIONr_angle_refined_deg0.8151.632719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1175257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.96926.29289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79615330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.481153
X-RAY DIFFRACTIONr_chiral_restr0.040.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021494
X-RAY DIFFRACTIONr_nbd_refined0.2070.2863
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21352
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2173
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1920.2138
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1350.298
X-RAY DIFFRACTIONr_mcbond_it1.4513.3141010
X-RAY DIFFRACTIONr_mcangle_it2.3344.971273
X-RAY DIFFRACTIONr_scbond_it1.753.435970
X-RAY DIFFRACTIONr_scangle_it2.7825.0971445
X-RAY DIFFRACTIONr_lrange_it7.03547.1773015
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
2-2.0510.445500.421955105994.90090.393
2.051-2.1060.415470.39928101995.6820.355
2.106-2.1660.43490.33189398895.34410.303
2.166-2.2310.382460.32389498095.91840.286
2.231-2.3020.364450.29485493696.0470.259
2.302-2.3810.316440.29184893195.8110.244
2.381-2.4680.287430.26281088196.82180.227
2.468-2.5660.288410.26378685796.49940.223
2.566-2.6770.307410.2776182597.21210.23
2.677-2.8030.236390.24173780296.75810.201
2.803-2.9490.253380.21570276496.85860.183
2.949-3.120.318350.20867372397.92530.171
3.12-3.3250.223330.17763868697.81340.141
3.325-3.5760.25320.14960664698.76160.116
3.576-3.8950.259310.14557661099.50820.118
3.895-4.3180.174280.13152255499.2780.108
4.318-4.9170.183250.1364785031000.114
4.917-5.8630.219220.15342344699.77580.127
5.863-7.7110.231190.18235037199.46090.144
7.711-14.8380.206140.152642781000.121

+
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