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- PDB-7qx4: mosquitocidal Cry11Aa determined at pH 7 from naturally-occurring... -

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Basic information

Entry
Database: PDB / ID: 7qx4
Titlemosquitocidal Cry11Aa 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 / SAD / Resolution: 2.6 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_PubMed / _citation.title
Revision 1.2Dec 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond / pdbx_related_exp_data_set

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pesticidal crystal protein Cry11Aa


Theoretical massNumber of molelcules
Total (without water)72,4071
Polymers72,4071
Non-polymers00
Water4,702261
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)289,6294
Polymers289,6294
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area9660 Å2
ΔGint-11 kcal/mol
Surface area97470 Å2
Unit cell
Length a, b, c (Å)57.640, 155.690, 171.140
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-706-

HOH

21A-952-

HOH

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Components

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


Mass: 72407.320 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.: 261 / 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: 2.65 Å3/Da / Density % sol: 53.61 %
Crystal growTemperature: 300 K / Method: in cell / pH: 7
Details: In cell crystallization by recombinant expression in the Bacillus thuringiensis serovar israelensis strain 4Q7 devoid of its pBt plasmid.

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Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.27 Å
DetectorType: CS-PAD CXI-2 / Detector: PIXEL / Date: Feb 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27 Å / Relative weight: 1
ReflectionResolution: 2.6→33.55 Å / Num. obs: 24198 / % possible obs: 99.9 % / Redundancy: 341.09 % / Biso Wilson estimate: 47.58 Å2 / CC1/2: 1 / R split: 0.107 / Net I/σ(I): 9.5
Reflection shellResolution: 2.6→2.66 Å / Redundancy: 230.58 % / Mean I/σ(I) obs: 1.16 / Num. unique obs: 1583 / CC1/2: 0.38 / R split: 0.954 / % possible all: 100
Serial crystallography measurementFocal spot size: 5 µm2 / Pulse duration: 50 fsec. / Pulse photon energy: 9.8 keV / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCarrier solvent: pure water / Crystal conc.: 40000000000 / Description: GVDN / Filter size: 20 µm / Injector nozzle: GDVN / Jet diameter: 6 µm / Power by: gas
Preparation: crystals rinsed and kept in water after sucrose gradient purification
Serial crystallography data reductionFrames indexed: 48652 / Frames total: 792623 / Lattices indexed: 1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
CRANK2phasing
PHENIX1.19.1refinement
PDB_EXTRACT3.27data extraction
CrystFEL0.8.0data reduction
CrystFEL0.8.0data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→33.55 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2412 1210 5 %
Rwork0.1715 22986 -
obs0.175 24196 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 202.8 Å2 / Biso mean: 50.6408 Å2 / Biso min: 19.98 Å2
Refinement stepCycle: final / Resolution: 2.6→33.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5014 0 0 261 5275
Biso mean---46.15 -
Num. residues----631
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6-2.70.34981320.277425072639
2.7-2.830.32981320.267225192651
2.83-2.980.34131320.256625092641
2.98-3.160.33411340.224425242658
3.16-3.410.29461340.200425462680
3.41-3.750.23581320.170325332665
3.75-4.290.21921360.144225632699
4.29-5.40.17491360.123725812717
5.4-33.550.18721420.135927042846

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