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Yorodumi- PDB-3c8b: Crystal structure of the catalytic domain of botulinum neurotoxin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c8b | ||||||
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Title | Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with inhibitory peptide RRGI | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / BOTULINUM NEUROTOXIN TYPE A / CATALYTIC DOMAIN / ENDOPEPTIDASE / BIO-WARFARE AGENT / METALLOPROTEASE / PROTEASE / SECRETED / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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: 1.47 Å | ||||||
Authors | Kumaran, D. / Swaminathan, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structure- and Substrate-based Inhibitor Design for Clostridium botulinum Neurotoxin Serotype A Authors: Kumaran, D. / Rawat, R. / Ludivico, M.L. / Ahmed, S.A. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c8b.cif.gz | 107.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c8b.ent.gz | 81.2 KB | Display | PDB format |
PDBx/mmJSON format | 3c8b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/3c8b ftp://data.pdbj.org/pub/pdb/validation_reports/c8/3c8b | HTTPS FTP |
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-Related structure data
Related structure data | 3bwiSC 3c88C 3c89C 3c8aC 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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-Components
#1: Protein | Mass: 49657.996 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-424 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (bacteria) / Strain: HALL / Gene: botA / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 RIL References: UniProt: A5HZZ9, UniProt: P0DPI1*PLUS, bontoxilysin | ||
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#2: Protein/peptide | Mass: 500.620 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Chemical | ChemComp-ZN / | ||
#4: Chemical | #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: 2.19 Å3/Da / Density % sol: 43.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 17% PEG 3350, 0.25M AMMONIUM SULFATE, 0.1M BIS-TRIS, pH 6.90, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→50 Å / Num. all: 63031 / Num. obs: 63031 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.1 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.47→1.51 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 3 / Num. unique all: 3135 / % possible all: 52.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BWI Resolution: 1.47→33.2 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 79982.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.3764 Å2 / ksol: 0.363297 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.47→33.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.47→1.56 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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