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Yorodumi- PDB-3ds9: A potent peptidomimetic inhibitor of botulinum neurotoxin serotyp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ds9 | ||||||
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Title | A potent peptidomimetic inhibitor of botulinum neurotoxin serotype A has a very different conformation than SNAP-25 substrate | ||||||
Components |
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Keywords | Hydrolase / Toxin / SNARE / botulism / inhibition / metalloprotease / neurotransmission / neuromuscular junction / Membrane / Metal-binding / Neurotoxin / Pharmaceutical / Protease / Secreted / 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: 1.758 Å | ||||||
Authors | Zuniga, J.E. / Fenn, T. | ||||||
Citation | Journal: Structure / Year: 2008 Title: A Potent Peptidomimetic Inhibitor of Botulinum Neurotoxin Serotype A Has a Very Different Conformation than SNAP-25 Substrate Authors: Zuniga, J.E. / Schmidt, J.J. / Fenn, T. / Burnett, J.C. / Arac, D. / Gussio, R. / Stafford, R.G. / Badie, S.S. / Bavari, S. / Brunger, A.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ds9.cif.gz | 173.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ds9.ent.gz | 144.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ds9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/3ds9 ftp://data.pdbj.org/pub/pdb/validation_reports/ds/3ds9 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47777.984 Da / Num. of mol.: 1 / Fragment: light chain / Mutation: residues 2-420 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (bacteria) / Strain: Hall / Gene: botA, CBO0806, CLC_0862 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: A5HZZ9, UniProt: P0DPI1*PLUS, bontoxilysin |
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#2: Protein/peptide | Mass: 1130.257 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: SNAP-25-derived peptide with three modified amino acids |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-NI / |
#5: 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: 2.42 Å3/Da / Density % sol: 49.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 0.1X PEG MME 2000, 5 mM NiCl2, and 100 mM HEPES pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.758→43.007 Å / Num. obs: 36042 / Redundancy: 5.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.758→43.007 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 25.93 / 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 / Bsol: 35.506 Å2 / ksol: 0.347 e/Å3 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.758→43.007 Å
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Refine LS restraints |
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