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Yorodumi- PDB-7qx6: mosquitocidal Cry11Aa-E583Q determined at pH 7 from naturally-occ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qx6 | |||||||||||||||||||||
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Title | mosquitocidal Cry11Aa-E583Q 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 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 | 7qx6.cif.gz | 121.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qx6.ent.gz | 96 KB | Display | PDB format |
PDBx/mmJSON format | 7qx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/7qx6 ftp://data.pdbj.org/pub/pdb/validation_reports/qx/7qx6 | HTTPS FTP |
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-Related structure data
Related structure data | 7qx4C 7qx5C 7qx7C 7qydC 7r1eC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 72406.328 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: 2.66 Å3/Da / Density % sol: 53.75 % |
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Crystal grow | Temperature: 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. |
-Data collection
Diffraction | Mean temperature: 300 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: European XFEL / Beamline: SPB/SFX / Wavelength: 1.33 Å |
Detector | Type: AGIPD / Detector: PIXEL / Date: Sep 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.33 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→23.5 Å / Num. obs: 12014 / % possible obs: 99.6 % / Redundancy: 267.2 % / CC1/2: 0.99 / R split: 0.211 / Net I/σ(I): 5.64 |
Reflection shell | Resolution: 3.3→3.38 Å / Mean I/σ(I) obs: 1.52 / Num. unique obs: 787 / CC1/2: 0.31 / R split: 0.802 / % possible all: 100 |
Serial crystallography measurement | Focal spot size: 1.3 µm2 |
Serial crystallography sample delivery | Method: injection |
Serial crystallography sample delivery injection | Carrier solvent: Pure water / Description: GVDN / Power by: gas Preparation: crystals rinsed and kept in water after sucrose gradient purification |
Serial crystallography data reduction | Frames indexed: 21833 / Frames total: 3523741 |
-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: D_1292119069 Resolution: 3.3→23.08 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24 / 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: 103.93 Å2 / Biso mean: 45.3094 Å2 / Biso min: 32.06 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.3→23.08 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %
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