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- PDB-7qyd: mosquitocidal Cry11Ba determined at pH 6.5 from naturally-occurri... -

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Basic information

Entry
Database: PDB / ID: 7qyd
Titlemosquitocidal Cry11Ba determined at pH 6.5 from naturally-occurring nanocrystals by Serial femtosecond crystallography
ComponentsPesticidal crystal protein Cry11Ba
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 Cry11Ba
Similarity search - Component
Biological speciesBacillus thuringiensis serovar jegathesan (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDe Zitter, E. / Tetreau, G. / Andreeva, E.A. / Coquelle, N. / Colletier, J.-P. / Sawaya, M.R. / Schibrowsky, N.A. / Cascio, D. / Rodriguez, J.A.
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 28, 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
Revision 1.3Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pesticidal crystal protein Cry11Ba
B: Pesticidal crystal protein Cry11Ba


Theoretical massNumber of molelcules
Total (without water)162,8252
Polymers162,8252
Non-polymers00
Water11,205622
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-2 kcal/mol
Surface area51810 Å2
Unit cell
Length a, b, c (Å)168.245, 158.528, 57.534
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Pesticidal crystal protein Cry11Ba / 81 kDa crystal protein / Crystaline entomocidal protoxin / Insecticidal delta-endotoxin CryXIB(a)


Mass: 81412.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar jegathesan (bacteria)
Gene: cry11Ba, cry11B, cryXIB(a)
Production host: Bacillus thuringiensis serovar israelensis (bacteria)
References: UniProt: Q45730
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 622 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 303 K / Method: in cell / pH: 6.5 / Details: crystallized in vivo

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.304373 Å
DetectorType: CS-PAD CXI-2 / Detector: PIXEL / Date: Sep 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.304373 Å / Relative weight: 1
ReflectionResolution: 2.4→42.1 Å / Num. obs: 61141 / % possible obs: 100 % / Redundancy: 57.9 % / CC1/2: 0.991 / R split: 0.0145 / Net I/σ(I): 4.7
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 17.1 % / Num. unique obs: 2980 / CC1/2: 0.359 / R split: 0.849 / % possible all: 100
Serial crystallography measurementFocal spot size: 1 µm2 / Pulse duration: 50 fsec. / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryDescription: microfluidic electrokinetic sample holder / Method: injection
Serial crystallography sample delivery injectionDescription: microfluidic electrokinetic sample holder
Serial crystallography data reductionLattices indexed: 19708

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
cctbx.xfeldata reduction
PHASERphasing
cctbx.xfeldata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QX4

7qx4


Resolution: 2.4→42.1 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: FREE R-VALUE / ESU R: 0.424 / ESU R Free: 0.253
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2309 5991 9.8 %
Rwork0.1826 55060 -
all0.187 --
obs-55060 99.92 %
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: 47.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.446 Å2-0 Å2-0 Å2
2---0.253 Å20 Å2
3---1.699 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10064 0 0 622 10686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01310330
X-RAY DIFFRACTIONr_bond_other_d0.0350.0179682
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.64414045
X-RAY DIFFRACTIONr_angle_other_deg2.2661.57722260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11251269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53122.777533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.513151700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8911554
X-RAY DIFFRACTIONr_chiral_restr0.0540.21383
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211764
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022516
X-RAY DIFFRACTIONr_nbd_refined0.1790.21790
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.28569
X-RAY DIFFRACTIONr_nbtor_refined0.1680.25103
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0680.24557
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2567
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0850.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1590.214
X-RAY DIFFRACTIONr_nbd_other0.2230.2106
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1430.213
X-RAY DIFFRACTIONr_mcbond_it3.4944.8555070
X-RAY DIFFRACTIONr_mcbond_other3.4874.8545069
X-RAY DIFFRACTIONr_mcangle_it5.2167.2676329
X-RAY DIFFRACTIONr_mcangle_other5.2167.2696330
X-RAY DIFFRACTIONr_scbond_it4.2535.2185260
X-RAY DIFFRACTIONr_scbond_other4.2535.2185261
X-RAY DIFFRACTIONr_scangle_it6.4117.6797712
X-RAY DIFFRACTIONr_scangle_other6.4117.687713
X-RAY DIFFRACTIONr_lrange_it7.98355.36211476
X-RAY DIFFRACTIONr_lrange_other7.96455.25811389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4630.364500.3293960X-RAY DIFFRACTION99.9094
2.463-2.5310.3464420.3053911X-RAY DIFFRACTION100
2.531-2.6040.3343740.293868X-RAY DIFFRACTION100
2.604-2.6840.2894090.2723681X-RAY DIFFRACTION100
2.684-2.7720.3044140.2513580X-RAY DIFFRACTION100
2.772-2.8690.2833870.2383492X-RAY DIFFRACTION100
2.869-2.9780.2824000.2193293X-RAY DIFFRACTION100
2.978-3.0990.2733520.2073237X-RAY DIFFRACTION100
3.099-3.2370.2333290.1843151X-RAY DIFFRACTION100
3.237-3.3950.2183450.1712983X-RAY DIFFRACTION100
3.395-3.5780.2062890.1652846X-RAY DIFFRACTION100
3.578-3.7950.2063040.1622679X-RAY DIFFRACTION100
3.795-4.0570.1932380.1532576X-RAY DIFFRACTION100
4.057-4.3810.1842620.1312381X-RAY DIFFRACTION100
4.381-4.7990.1582230.1252229X-RAY DIFFRACTION100
4.799-5.3640.1752250.1241962X-RAY DIFFRACTION100
5.364-6.1920.2381980.1471785X-RAY DIFFRACTION100
6.192-7.5780.2151410.1671552X-RAY DIFFRACTION100
7.578-10.6940.1851260.1321213X-RAY DIFFRACTION100
10.694-42.10.197830.19681X-RAY DIFFRACTION94.6716
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: -0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
123.275739.16542.9682
2-24.991839.981325.4671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA12 - 658
2X-RAY DIFFRACTION2ALLB16 - 656

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