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Yorodumi- PDB-4el4: Crystal structure of the catalytic domain of botulinum neurotoxin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4el4 | ||||||
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Title | Crystal structure of the catalytic domain of botulinum neurotoxin BoNT/A C134S/C165S double mutant | ||||||
Components | Botulinum neurotoxin A light chain | ||||||
Keywords | HYDROLASE / Metalloprotease / peptidase M27 superfamily / Clostridial neurotoxin zinc protease / Human target snap-25 | ||||||
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 / RIGID BODY / Resolution: 1.2 Å | ||||||
Authors | Stura, E.A. / Vera, L. / Ptchelkine, D. / Dive, V. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structural Framework for Covalent Inhibition of Clostridium botulinum Neurotoxin A by Targeting Cys165. Authors: Stura, E.A. / Le Roux, L. / Guitot, K. / Garcia, S. / Bregant, S. / Beau, F. / Vera, L. / Collet, G. / Ptchelkine, D. / Bakirci, H. / Dive, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4el4.cif.gz | 219.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4el4.ent.gz | 172.6 KB | Display | PDB format |
PDBx/mmJSON format | 4el4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/4el4 ftp://data.pdbj.org/pub/pdb/validation_reports/el/4el4 | HTTPS FTP |
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-Related structure data
Related structure data | 4ej5SC 4elcC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 50873.254 Da / Num. of mol.: 1 / Fragment: UNP residues 1-425 / Mutation: C134S, C165S Source method: isolated from a genetically manipulated source Details: expression vector between Nde I and Sal I restriction sites, generating a thrombin cleavable N-terminal 6His affinity tag Source: (gene. exp.) Clostridium botulinum (bacteria) / Strain: Hall ATCC 3502 / Gene: atx, bna, bont/a, botA / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 References: UniProt: P10845, UniProt: P0DPI1*PLUS, bontoxilysin |
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-Non-polymers , 5 types, 571 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / | #6: 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: 2.06 Å3/Da / Density % sol: 40.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: reservoir: 29% MPEG2K, 0.04 M Li2SO4, 0.1 M imidazole-HCl pH 6.0, cryoprotectant: 18% MPEG2K, 22% MPD, 10% DMSO, 0.050 M bicine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2009 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→46.08 Å / Num. all: 130060 / Num. obs: 128420 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.97 % / Biso Wilson estimate: 17.075 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.066 / Net I/σ(I): 11.11 |
Reflection shell | Resolution: 1.2→1.27 Å / Redundancy: 3.86 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 1.99 / Num. unique all: 21021 / Rsym value: 0.695 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: RIGID BODY Starting model: PDB entry 4EJ5 Resolution: 1.2→46.08 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.944 / SU ML: 0.038 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.046 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.829 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→46.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20
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