[English] 日本語
Yorodumi
- PDB-7qx5: mosquitocidal Cry11Aa-Y449F determined at pH 7 from naturally-occ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qx5
Titlemosquitocidal Cry11Aa-Y449F determined at pH 7 from naturally-occurring nanocrystals by Serial femtosecond crystallography
ComponentsPesticidal crystal protein Cry11Aa
KeywordsTOXIN / naturally-occurring crystals mosquitocidal toxin serial femtosecond crystallography
Function / homology
Function and homology information


symbiont-mediated killing of host cell / sporulation resulting in formation of a cellular spore / toxin activity
Similarity search - Function
Pesticidal crystal protein, N-terminal domain / Pesticidal crystal protein / Pesticidal crystal protein, N-terminal / Pesticidal crystal protein, N-terminal domain superfamily / delta endotoxin, N-terminal domain / Delta-Endotoxin; domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Pesticidal crystal protein Cry11Aa
Similarity search - Component
Biological speciesBacillus thuringiensis serovar israelensis (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsDe Zitter, E. / Tetreau, G. / Andreeva, E.A. / Coquelle, N. / Colletier, J.-P.
Funding support France, 6items
OrganizationGrant numberCountry
French National Research AgencyANR-17-CE11-0018-01 France
Agence Nationale de la Recherche (ANR)ANR-2018-CE11-0005-02 France
Centre National de la Recherche Scientifique (CNRS) France
Grenoble Instruct-ERIC Center (ISBG) France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05-02 France
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)ANR-17-EURE-0003 France
CitationJournal: Nat Commun / Year: 2022
Title: De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystals.
Authors: Tetreau, G. / Sawaya, M.R. / De Zitter, E. / Andreeva, E.A. / Banneville, A.S. / Schibrowsky, N.A. / Coquelle, N. / Brewster, A.S. / Grunbein, M.L. / Kovacs, G.N. / Hunter, M.S. / Kloos, M. ...Authors: Tetreau, G. / Sawaya, M.R. / De Zitter, E. / Andreeva, E.A. / Banneville, A.S. / Schibrowsky, N.A. / Coquelle, N. / Brewster, A.S. / Grunbein, M.L. / Kovacs, G.N. / Hunter, M.S. / Kloos, M. / Sierra, R.G. / Schiro, G. / Qiao, P. / Stricker, M. / Bideshi, D. / Young, I.D. / Zala, N. / Engilberge, S. / Gorel, A. / Signor, L. / Teulon, J.M. / Hilpert, M. / Foucar, L. / Bielecki, J. / Bean, R. / de Wijn, R. / Sato, T. / Kirkwood, H. / Letrun, R. / Batyuk, A. / Snigireva, I. / Fenel, D. / Schubert, R. / Canfield, E.J. / Alba, M.M. / Laporte, F. / Despres, L. / Bacia, M. / Roux, A. / Chapelle, C. / Riobe, F. / Maury, O. / Ling, W.L. / Boutet, S. / Mancuso, A. / Gutsche, I. / Girard, E. / Barends, T.R.M. / Pellequer, J.L. / Park, H.W. / Laganowsky, A.D. / Rodriguez, J. / Burghammer, M. / Shoeman, R.L. / Doak, R.B. / Weik, M. / Sauter, N.K. / Federici, B. / Cascio, D. / Schlichting, I. / Colletier, J.P.
History
DepositionJan 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: 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 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pesticidal crystal protein Cry11Aa


Theoretical massNumber of molelcules
Total (without water)72,3911
Polymers72,3911
Non-polymers00
Water23413
1
A: Pesticidal crystal protein Cry11Aa

A: Pesticidal crystal protein Cry11Aa

A: Pesticidal crystal protein Cry11Aa

A: Pesticidal crystal protein Cry11Aa


Theoretical massNumber of molelcules
Total (without water)289,5654
Polymers289,5654
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_756-x+2,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area9320 Å2
ΔGint-36 kcal/mol
Surface area98300 Å2
Unit cell
Length a, b, c (Å)57.730, 155.550, 171.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-701-

HOH

-
Components

#1: Protein Pesticidal crystal protein Cry11Aa / 72 kDa crystal protein / Crystaline entomocidal protoxin / Insecticidal delta-endotoxin CryXIA(a)


Mass: 72391.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar israelensis (bacteria)
Gene: cry11Aa, cryD, cryIVd, cryXIA(a) / Plasmid: pWF53
Production host: Bacillus thuringiensis serovar israelensis (bacteria)
Strain (production host): 4Q7 / References: UniProt: P21256
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.66 Å3/Da / Density % sol: 53.75 %
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: European XFEL / Beamline: SPB/SFX / Wavelength: 1.33 Å
DetectorType: AGIPD / Detector: PIXEL / Date: Sep 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.33 Å / Relative weight: 1
ReflectionResolution: 3.1→23.78 Å / Num. obs: 14447 / % possible obs: 99.7 % / Redundancy: 1403.7 % / CC1/2: 1 / R split: 0.118 / Net I/σ(I): 9.95
Reflection shellResolution: 3.1→3.17 Å / Mean I/σ(I) obs: 1.35 / Num. unique obs: 950 / CC1/2: 0.6 / R split: 0.896 / % possible all: 100
Serial crystallography measurementFocal spot size: 1.3 µm2 / Pulse photon energy: 9.3 keV
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCarrier solvent: pure water / Description: GVDN / Power by: gas
Preparation: crystals rinsed and kept in water after sucrose gradient purification
Serial crystallography data reductionFrames indexed: 104359 / Frames total: 5993679 / Lattices indexed: 1

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.93 Å23.42 Å

-
Processing

Software
NameVersionClassification
PHASER2.8.3phasing
PHENIX1.18.2refinement
PDB_EXTRACT3.27data extraction
CrystFEL0.8.0data reduction
CrystFEL0.8.0data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1292119069

Resolution: 3.1→23.18 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 723 5.01 %
Rwork0.2241 13719 -
obs0.2256 14442 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.27 Å2 / Biso mean: 42.9253 Å2 / Biso min: 30.99 Å2
Refinement stepCycle: final / Resolution: 3.1→23.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4956 0 0 13 4969
Biso mean---58.72 -
Num. residues----627
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.1-3.340.39391430.359126982841
3.34-3.670.29911410.283226872828
3.67-4.20.24451430.234127282871
4.2-5.280.23461450.187527512896
5.29-23.180.19821510.165428553006

+
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