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Yorodumi- PDB-3fuo: The Crystal structure of receptor binding domain of botulinum neu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fuo | ||||||
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Title | The Crystal structure of receptor binding domain of botulinum neurotoxin serotype A | ||||||
Components | Botulinum neurotoxin type A | ||||||
Keywords | HYDROLASE / Botulinum Neurotoxin / Ganglioside Binding / Membrane / Metal-binding / Metalloprotease / Neurotoxin / Pharmaceutical / Protease / Secreted / Toxin / Transmembrane / Zinc | ||||||
Function / homology | Function and homology information host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 ...host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Clostridium botulinum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Fu, Z. / Chen, C. / Barbieri, J.T. / Kim, J.-J.P. / Baldwin, M.R. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Glycosylated SV2 and gangliosides as dual receptors for botulinum neurotoxin serotype F Authors: Fu, Z. / Chen, C. / Barbieri, J.T. / Kim, J.J. / Baldwin, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fuo.cif.gz | 102.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fuo.ent.gz | 76.5 KB | Display | PDB format |
PDBx/mmJSON format | 3fuo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/3fuo ftp://data.pdbj.org/pub/pdb/validation_reports/fu/3fuo | HTTPS FTP |
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-Related structure data
Related structure data | 3fuqC 3tbaS 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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Details | monomer |
-Components
#1: Protein | Mass: 49751.332 Da / Num. of mol.: 1 / Fragment: sequence database residues 871-1296 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: atx, bna, botA, Botulinum Neurotoxin A / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 References: UniProt: P10845, UniProt: P0DPI1*PLUS, bontoxilysin |
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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: 2.36 Å3/Da / Density % sol: 47.84 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 0.1 M Hepes pH 7.6, 12% PEG8K, 8% glycerol and 0.1 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2006 |
Radiation | Monochromator: Ge 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→18.92 Å / Num. obs: 42220 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.3 Å2 / Rsym value: 0.069 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 4187 / Rsym value: 0.56 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3TBA Resolution: 1.8→18.92 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 166769.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Bulk Solvent Model Used
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.0204 Å2 / ksol: 0.385267 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→18.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
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Xplor file |
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