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Yorodumi- PDB-7qx4: mosquitocidal Cry11Aa determined at pH 7 from naturally-occurring... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qx4 | |||||||||||||||||||||
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Title | mosquitocidal Cry11Aa determined at pH 7 from naturally-occurring nanocrystals by Serial femtosecond crystallography | |||||||||||||||||||||
Components | Pesticidal crystal protein Cry11Aa | |||||||||||||||||||||
Keywords | TOXIN / naturally-occurring crystals mosquitocidal toxin serial femtosecond crystallography | |||||||||||||||||||||
Function / homology | Pesticidal 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 species | Bacillus thuringiensis serovar israelensis (bacteria) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / SAD / Resolution: 2.6 Å | |||||||||||||||||||||
Authors | De Zitter, E. / Tetreau, G. / Andreeva, E.A. / Coquelle, N. / Colletier, J.-P. | |||||||||||||||||||||
Funding support | France, 6items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qx4.cif.gz | 147.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qx4.ent.gz | 112.2 KB | Display | PDB format |
PDBx/mmJSON format | 7qx4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/7qx4 ftp://data.pdbj.org/pub/pdb/validation_reports/qx/7qx4 | HTTPS FTP |
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-Related structure data
Related structure data | 7qx5C 7qx6C 7qx7C 7qydC 7r1eC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.11577/1873154 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.61 % |
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Crystal grow | Temperature: 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. |
-Data collection
Diffraction | Mean temperature: 300 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.27 Å |
Detector | Type: CS-PAD CXI-2 / Detector: PIXEL / Date: Feb 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.27 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 measurement | Focal spot size: 5 µm2 / Pulse duration: 50 fsec. / Pulse photon energy: 9.8 keV / XFEL pulse repetition rate: 120 Hz |
Serial crystallography sample delivery | Method: injection |
Serial crystallography sample delivery injection | Carrier 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 reduction | Frames indexed: 48652 / Frames total: 792623 / Lattices indexed: 1 |
-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 202.8 Å2 / Biso mean: 50.6408 Å2 / Biso min: 19.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→33.55 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %
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