+Open data
-Basic information
Entry | Database: PDB / ID: 1i5p | ||||||
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Title | INSECTICIDAL CRYSTAL PROTEIN CRY2AA | ||||||
Components | PESTICIDIAL CRYSTAL PROTEIN CRY2AA | ||||||
Keywords | TOXIN / HELICAL BUNDLE / BETA PRISM / LECTIN-LIKE BETA SANDWICH / JELLY ROLL | ||||||
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 serovar kurstaki (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å | ||||||
Authors | Morse, R.J. / Stroud, R.M. / Yamamoto, T. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Structure of Cry2Aa suggests an unexpected receptor binding epitope. Authors: Morse, R.J. / Yamamoto, T. / Stroud, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i5p.cif.gz | 140 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i5p.ent.gz | 113.5 KB | Display | PDB format |
PDBx/mmJSON format | 1i5p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/1i5p ftp://data.pdbj.org/pub/pdb/validation_reports/i5/1i5p | 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: 70907.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thuringiensis serovar kurstaki (bacteria) Species: Bacillus thuringiensis / Strain: HD-1 / Gene: CRY2AA OPERON / Plasmid: PTZ18R / Production host: Bacillus thuringiensis (bacteria) / Strain (production host): CRYB / References: UniProt: P0A377 |
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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: 2.12 Å3/Da / Density % sol: 41.88 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Tris-HCL, EDTA, NH4OH, mercaptoethonanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 22, 1993 |
Radiation | Monochromator: HORIZONTALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→27.97 Å / Num. obs: 31509 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.2→2.34 Å / Redundancy: 7 % / Rmerge(I) obs: 0.131 / % possible all: 98.9 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 27.97 Å / Observed criterion σ(I): 0 / Redundancy: 8 % / Num. measured all: 245580 |
Reflection shell | *PLUS Redundancy: 7 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.2→27.97 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4370488 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.1827 Å2 / ksol: 0.378356 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→27.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.225 / Rfactor Rwork: 0.177 / Rfactor obs: 0.21 |