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- PDB-4ej5: Crystal structure of the catalytic domain of botulinum neurotoxin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ej5 | ||||||
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Title | Crystal structure of the catalytic domain of botulinum neurotoxin BoNT/A wild-type | ||||||
![]() | Botulinum neurotoxin A light chain | ||||||
![]() | HYDROLASE / Metalloprotease / peptidase M27 superfamily / Clostridial neurotoxin zinc protease / Human target snap-25 | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stura, E.A. / Vera, L. / Dive, V. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.9 KB | Display | ![]() |
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PDB format | ![]() | 84.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 486.3 KB | Display | ![]() |
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Full document | ![]() | 492.7 KB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 32.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4el4C ![]() 4elcC ![]() 2ilpS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 50905.379 Da / Num. of mol.: 1 / Fragment: UNP residues 1-425 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.) ![]() ![]() ![]() ![]() References: UniProt: P10845, UniProt: P0DPI1*PLUS, bontoxilysin |
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-Non-polymers , 7 types, 395 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||||||
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#3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-IMD / | #6: Chemical | ChemComp-CO3 / | #7: Chemical | ChemComp-GOL / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 8.3% monomethyl polyethylene glycol 2000, 0.17 M lithium sulfate, 6.25% 4,2 methyl pentane diol, 0.1 M imidazole malate, pH 6.0, cryoprotectant: 18% MPEG2K, 22% MPD, 10% DMSO, .050 M bicine, ...Details: 8.3% monomethyl polyethylene glycol 2000, 0.17 M lithium sulfate, 6.25% 4,2 methyl pentane diol, 0.1 M imidazole malate, pH 6.0, cryoprotectant: 18% MPEG2K, 22% MPD, 10% DMSO, .050 M bicine, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 29, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→42.17 Å / Num. all: 34715 / Num. obs: 34616 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.19 % / Biso Wilson estimate: 25.086 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.052 / Net I/σ(I): 22.27 |
Reflection shell | Resolution: 1.87→1.98 Å / Redundancy: 4.17 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 4.83 / Num. unique all: 5551 / Rsym value: 0.363 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2ILP Resolution: 1.87→42.166 Å / SU ML: 0.48 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): -3 / Phase error: 19.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.788 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.268 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→42.166 Å
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Refine LS restraints |
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LS refinement shell |
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