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Yorodumi- PDB-6ovb: Crystal structure of a Bacillus thuringiensis Cry1Da tryptic core... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ovb | ||||||
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Title | Crystal structure of a Bacillus thuringiensis Cry1Da tryptic core variant | ||||||
Components | Active core crystal toxin protein 1D | ||||||
Keywords | TOXIN / Bacillus thuringiensis / Cry toxin / B.t. | ||||||
Function / homology | Function and homology information sporulation resulting in formation of a cellular spore / : / toxin activity / signaling receptor binding Similarity search - Function | ||||||
Biological species | Bacillus thuringiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.611 Å | ||||||
Authors | Rydel, T.J. / Halls, C. / Evdokimov, A.G. / Beishir, S.C. | ||||||
Citation | Journal: Appl.Environ.Microbiol. / Year: 2019 Title: Bacillus thuringiensis Cry1Da_7 and Cry1B.868 Protein Interactions with Novel Receptors Allow Control of Resistant Fall Armyworms, Spodoptera frugiperda (J.E. Smith). Authors: Wang, Y. / Wang, J. / Fu, X. / Nageotte, J.R. / Silverman, J. / Bretsnyder, E.C. / Chen, D. / Rydel, T.J. / Bean, G.J. / Li, K.S. / Kraft, E. / Gowda, A. / Nance, A. / Moore, R.G. / Pleau, M. ...Authors: Wang, Y. / Wang, J. / Fu, X. / Nageotte, J.R. / Silverman, J. / Bretsnyder, E.C. / Chen, D. / Rydel, T.J. / Bean, G.J. / Li, K.S. / Kraft, E. / Gowda, A. / Nance, A. / Moore, R.G. / Pleau, M.J. / Milligan, J.S. / Anderson, H.M. / Asiimwe, P. / Evans, A. / Moar, W.J. / Martinelli, S. / Head, G.P. / Haas, J.A. / Baum, J.A. / Yang, F. / Kerns, D.L. / Jerga, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ovb.cif.gz | 135.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ovb.ent.gz | 102.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ovb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/6ovb ftp://data.pdbj.org/pub/pdb/validation_reports/ov/6ovb | HTTPS FTP |
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-Related structure data
Related structure data | 6owkC 4arxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure 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: 64964.965 Da / Num. of mol.: 1 / Fragment: UNP residues 27-603 / Mutation: V108C, E128C, S282V, Y316S, I368P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Production host: Bacillus thuringiensis (bacteria) / References: UniProt: I3RS06, UniProt: P19415*PLUS |
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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: 4.46 Å3/Da / Density % sol: 68.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M sodium acetate, pH 4.0, 10% PGME 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jul 8, 2013 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.611→44.62 Å / Num. obs: 35721 / % possible obs: 99.98 % / Redundancy: 10.7 % / Biso Wilson estimate: 27.69 Å2 / Rmerge(I) obs: 0.167 / Net I/σ(I): 19.25 |
Reflection shell | Resolution: 2.6112→2.7045 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 3537 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4ARX Resolution: 2.611→41.307 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.26 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.611→41.307 Å
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Refine LS restraints |
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LS refinement shell |
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