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- PDB-7qx7: mosquitocidal Cry11Aa-F17Y determined at pH 7 from naturally-occu... -

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Basic information

Entry
Database: PDB / ID: 7qx7
Titlemosquitocidal Cry11Aa-F17Y 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 / homologyPesticidal crystal protein / symbiont-mediated killing of host cell / Pesticidal crystal protein, N-terminal / Pesticidal crystal protein, N-terminal domain superfamily / delta endotoxin, N-terminal domain / sporulation resulting in formation of a cellular spore / toxin activity / Pesticidal crystal protein Cry11Aa
Function and homology information
Biological speciesBacillus thuringiensis serovar israelensis (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.4 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

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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)72,4231
Polymers72,4231
Non-polymers00
Water905
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)289,6934
Polymers289,6934
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 area9960 Å2
ΔGint-26 kcal/mol
Surface area97860 Å2
Unit cell
Length a, b, c (Å)57.720, 155.390, 171.660
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

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Components

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


Mass: 72423.320 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 / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.66 Å3/Da / Density % sol: 53.71 %
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.

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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: 3.4→23.17 Å / Num. obs: 10990 / % possible obs: 99.6 % / Redundancy: 265.7 % / CC1/2: 0.96 / R split: 0.197 / Net I/σ(I): 6.31
Reflection shellResolution: 3.4→3.48 Å / Num. unique obs: 707 / CC1/2: 0.31 / R split: 0.802
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: 28227 / Frames total: 3150500 / Lattices indexed: 1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.84 Å23.22 Å

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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: 3.4→23.17 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2512 551 5.02 %
Rwork0.2124 10435 -
obs0.2144 10986 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.59 Å2 / Biso mean: 54.4002 Å2 / Biso min: 41.7 Å2
Refinement stepCycle: final / Resolution: 3.4→23.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4970 0 0 5 4975
Biso mean---52.38 -
Num. residues----630
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.4-3.740.32961360.296325422678
3.74-4.280.28221330.239425842717
4.28-5.380.22661380.183326022740
5.38-23.170.21381440.179927072851

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