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- PDB-7r1e: Mosquitocidal Cry11Ba determined at pH 10.4 from naturally-occurr... -

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Basic information

Entry
Database: PDB / ID: 7r1e
TitleMosquitocidal Cry11Ba determined at pH 10.4 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 / FOURIER SYNTHESIS / Resolution: 2.65 Å
AuthorsColletier, 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
DepositionFeb 2, 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 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)163,0094
Polymers162,8252
Non-polymers1842
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-0 kcal/mol
Surface area49130 Å2
Unit cell
Length a, b, c (Å)167.499, 157.992, 57.428
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 303 K / Method: in cell / pH: 10.4 / 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: 1.303351 Å
DetectorType: CS-PAD CXI-2 / Detector: PIXEL / Date: Nov 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.303351 Å / Relative weight: 1
ReflectionResolution: 2.65→35.72 Å / Num. obs: 45243 / % possible obs: 99.4 % / Redundancy: 77 % / Biso Wilson estimate: 32.2 Å2 / CC1/2: 0.985 / R split: 0.224 / Net I/σ(I): 3.98
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 21 % / Mean I/σ(I) obs: 1.02 / Num. unique obs: 2204 / CC1/2: 0.152 / R split: 0.84 / % possible all: 100
Serial crystallography measurementFocal spot size: 1 µm2 / Pulse duration: 41 fsec. / Pulse energy: 1.1 µJ / Pulse photon energy: 9.5 keV / Source distance: 140 m / Source size: 1 µm2 / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryDescription: microfluidic electrokinetic sample holder / Method: injection
Serial crystallography sample delivery injectionCarrier solvent: 50% glycerol, 0.1M CAPS buffer pH 10.4 / Description: microfluidic electrokinetic sample holder / Flow rate: 1 µL/min
Serial crystallography data reductionLattices indexed: 15689

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
cctbx.xfeldata reduction
cctbx.primedata scaling
PHENIX1.20_4459phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7QYD

7qyd


Resolution: 2.65→35.72 Å / SU ML: 0.4167 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.2186
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2473 4525 10 %
Rwork0.2365 40703 -
obs0.2376 45228 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.39 Å2
Refinement stepCycle: LAST / Resolution: 2.65→35.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9900 0 12 119 10031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001510150
X-RAY DIFFRACTIONf_angle_d0.408313794
X-RAY DIFFRACTIONf_chiral_restr0.0411538
X-RAY DIFFRACTIONf_plane_restr0.00331766
X-RAY DIFFRACTIONf_dihedral_angle_d10.64323656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.680.40991450.36621346X-RAY DIFFRACTION100
2.68-2.710.35161580.36131340X-RAY DIFFRACTION100
2.71-2.740.34721450.37031337X-RAY DIFFRACTION100
2.74-2.780.36821460.34141311X-RAY DIFFRACTION100
2.78-2.820.34731630.36481328X-RAY DIFFRACTION100
2.82-2.850.34421500.35681359X-RAY DIFFRACTION100
2.85-2.90.32591490.34111342X-RAY DIFFRACTION100
2.9-2.940.29491500.32851310X-RAY DIFFRACTION100
2.94-2.980.29851490.31031331X-RAY DIFFRACTION100
2.98-3.030.31271310.31051378X-RAY DIFFRACTION100
3.03-3.090.31391460.31421311X-RAY DIFFRACTION100
3.09-3.140.31971280.30971373X-RAY DIFFRACTION100
3.14-3.20.29161490.29291381X-RAY DIFFRACTION100
3.2-3.270.30041460.27821307X-RAY DIFFRACTION100
3.27-3.340.31281520.27521353X-RAY DIFFRACTION100
3.34-3.420.26221490.26141344X-RAY DIFFRACTION100
3.42-3.50.27061630.261331X-RAY DIFFRACTION99.93
3.5-3.60.26871560.22861367X-RAY DIFFRACTION100
3.6-3.70.23311620.21271308X-RAY DIFFRACTION99.93
3.7-3.820.21951740.2131370X-RAY DIFFRACTION100
3.82-3.960.21751520.21551323X-RAY DIFFRACTION99.93
3.96-4.120.22711510.19681379X-RAY DIFFRACTION100
4.12-4.30.18771580.17441328X-RAY DIFFRACTION100
4.3-4.530.20011410.16531389X-RAY DIFFRACTION100
4.53-4.810.17121500.15941378X-RAY DIFFRACTION99.93
4.81-5.180.17331620.15761357X-RAY DIFFRACTION99.93
5.18-5.70.19421320.18311404X-RAY DIFFRACTION100
5.7-6.520.20821680.20321383X-RAY DIFFRACTION100
6.52-8.20.18731600.20521425X-RAY DIFFRACTION100
8.2-35.720.2151400.18661510X-RAY DIFFRACTION99.4
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3488863265040.184198566957-0.1756926568180.0768286247521-0.0518783469630.255369134064-0.0396316099163-0.03489684104630.18513266352-0.01550503350230.005971166662840.03832744036970.1629662657220.0592597497212-0.02037223149310.290778442370.128213674556-0.001988370520130.277781341937-0.03561859199730.28003305367723.588399950738.68572789372.70757322577
20.547390415091-0.00112605671711-0.2751990669460.0688602575789-0.07998168783210.191091123137-0.03357929862430.009352789713430.275474604778-0.0279523316345-0.0103589403172-0.1783022320170.223280470845-0.0378291840174-0.0597441775590.30165289388-0.1353333236110.006750373219210.2381728347560.06219061426850.103270444975-24.735259247739.375355703725.6614268318
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA - C12 - 8011
22chain BBD17 - 6551 - 621

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