+Open data
-Basic information
Entry | Database: PDB / ID: 1cby | ||||||
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Title | DELTA-ENDOTOXIN | ||||||
Components | DELTA-ENDOTOXIN CYTB | ||||||
Keywords | TOXIN / MOSQUITOCIDAL / MEMBRANE PORE / CYTOLYTIC | ||||||
Function / homology | Function and homology information sporulation resulting in formation of a cellular spore / : / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Bacillus thuringiensis serovar kyushuensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å | ||||||
Authors | Li, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: Structure of the mosquitocidal delta-endotoxin CytB from Bacillus thuringiensis sp. kyushuensis and implications for membrane pore formation. Authors: Li, J. / Koni, P.A. / Ellar, D.J. #1: Journal: Proteins / Year: 1995 Title: Crystallization of a Membrane Pore-Forming Protein with Mosquitocidal Activity from Bacillus Thuringiensis Subsp. Kyushuensis Authors: Li, J. / Koni, P.A. / Ellar, D.J. #2: Journal: Microbiology (Reading, Engl.) / Year: 1994 Title: Biochemical Characterization of Bacillus Thuringiensis Cytolytic Delta-Endotoxins Authors: Koni, P.A. / Ellar, D.J. #3: Journal: J.Mol.Biol. / Year: 1993 Title: Cloning and Characterization of a Novel Bacillus Thuringiensis Cytolytic Delta-Endotoxin Authors: Koni, P.A. / Ellar, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cby.cif.gz | 57.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cby.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 1cby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/1cby ftp://data.pdbj.org/pub/pdb/validation_reports/cb/1cby | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29260.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thuringiensis serovar kyushuensis (bacteria) Species: Bacillus thuringiensis / Strain: KYUSHUENSIS / Gene: CYTB / Plasmid: PCYTB / Gene (production host): CYTB / Production host: Escherichia coli (E. coli) / References: UniProt: Q04470 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 33 % | |||||||||||||||
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Crystal grow | *PLUS pH: 8.5 / Method: microdialysis | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 25, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→19 Å / Num. obs: 7235 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.071 |
-Processing
Software |
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Refinement | Resolution: 2.6→19 Å / σ(F): 0
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Displacement parameters | Biso mean: 32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→19 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 2.78 Å / Rfactor Rfree: 0.347 / Rfactor obs: 0.304 |