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Yorodumi- PDB-2g7k: Structure of the Light Chain of Botulinum Neurotoxin, Serotype A ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g7k | ||||||
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Title | Structure of the Light Chain of Botulinum Neurotoxin, Serotype A Bound to small Molecule Inhibitors | ||||||
Components | Botulinum neurotoxin type A | ||||||
Keywords | HYDROLASE / Botulinum neurotoxin / zinc protease / SNAP25 | ||||||
Function / homology | Function and homology information bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / zinc ion binding ...bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Clostridium botulinum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Fu, Z. / Baldwin, M.R. / Boldt, G.E. / Crawford, A. / Janda, K.D. / Barbieri, J.T. / Kim, J.-J.P. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Light chain of botulinum neurotoxin serotype A: structural resolution of a catalytic intermediate. Authors: Fu, Z. / Chen, S. / Baldwin, M.R. / Boldt, G.E. / Crawford, A. / Janda, K.D. / Barbieri, J.T. / Kim, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g7k.cif.gz | 167.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g7k.ent.gz | 134.9 KB | Display | PDB format |
PDBx/mmJSON format | 2g7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/2g7k ftp://data.pdbj.org/pub/pdb/validation_reports/g7/2g7k | HTTPS FTP |
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-Related structure data
Related structure data | 2g7pC 2g7qC 1e1hS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 48810.887 Da / Num. of mol.: 2 / Fragment: Light Chain A, residues 2-425 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botA, atx, bna / Plasmid: PET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21RIL(DE3) / References: UniProt: Q45894, bontoxilysin |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.18 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.1M HEPES buffer, 30% PEG1500, 0.1M NaCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 20, 2005 / Details: Mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. all: 32204 / Num. obs: 32204 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.6 Å2 / Rsym value: 0.124 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E1H, MONOMER Resolution: 2.8→29.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 239473.14 / 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: 29.6308 Å2 / ksol: 0.344849 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→29.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.9 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
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Xplor file |
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