+Open data
-Basic information
Entry | Database: PDB / ID: 5ghe | ||||||
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Title | Crystal Structure of Bacillus thuringiensis Cry6Aa2 Protoxin | ||||||
Components | Pesticidal crystal protein Cry6Aa | ||||||
Keywords | TOXIN / Cry6Aa2 / ClyA-type / Bacillus thuringiensis | ||||||
Function / homology | sporulation resulting in formation of a cellular spore / toxin activity / killing of cells of another organism / host cell plasma membrane / extracellular region / membrane / Pesticidal crystal protein Cry6Aa Function and homology information | ||||||
Biological species | Bacillus thuringiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.901 Å | ||||||
Authors | Huang, J. / Guan, Z. / Zou, T. / Sun, M. / Yin, P. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2016 Title: Crystal structure of Cry6Aa: A novel nematicidal ClyA-type alpha-pore-forming toxin from Bacillus thuringiensis Authors: Huang, J. / Guan, Z. / Wan, L. / Zou, T. / Sun, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ghe.cif.gz | 172.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ghe.ent.gz | 135.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ghe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/5ghe ftp://data.pdbj.org/pub/pdb/validation_reports/gh/5ghe | 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: 48232.969 Da / Num. of mol.: 1 / Fragment: UNP residues 1-401 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: cry6Aa, cryVIa, cryVIA(a) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q45757 |
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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: 2.44 Å3/Da / Density % sol: 49.57 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: Glycerol, PEG 100, Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.92 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→45 Å / Num. obs: 36545 / % possible obs: 99.8 % / Redundancy: 11.3 % / Net I/σ(I): 17.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.901→44.01 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.89 / 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: 1.901→44.01 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -31.7249 Å / Origin y: -11.4247 Å / Origin z: -0.7188 Å
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Refinement TLS group | Selection details: all |