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- PDB-4kuf: 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: 4kuf | ||||||
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Title | Crystal structure of the catalytic domain of botulinum neurotoxin BoNT/A C134 mutant with MTSEA modified Cys-165 causing stretch disorder | ||||||
![]() | Botulinum neurotoxin A light chain | ||||||
![]() | HYDROLASE / Clostridial neurotoxin zinc protease / Peptidase_M27 / SNAP 25 / covalent inhibition | ||||||
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. / Ptchelkine, D. / Bakirci, H. / Garcia, S. / Dive, V. | ||||||
![]() | ![]() Title: Covalent modification of the active site cysteine stresses Clostridium botulinum neurotoxin A Authors: Guitot, K. / Vera, L. / Le Roux, L. / Bregant, S. / Ptchelkine, D. / Beau, F. / Stura, E.A. / 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 | ![]() | 115.6 KB | Display | ![]() |
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PDB format | ![]() | 86.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 487.8 KB | Display | ![]() |
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Full document | ![]() | 493 KB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 31.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ks6C ![]() 4ktxC ![]() 4elcS 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 50964.449 Da / Num. of mol.: 1 / Fragment: Catalytic domain residues 1-425 / Mutation: C134S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A5HZZ9, UniProt: P0DPI1*PLUS, bontoxilysin |
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-Non-polymers , 7 types, 350 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/LMR.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/LMR.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||||||
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#3: Chemical | ChemComp-DMS / #4: Chemical | ChemComp-LMR / ( | #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-EDO / #7: Chemical | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: LCA-C134S-MTSEA at 3 mg/ml in 0.010 M Tris-HCl, pH 7.9, 0.050 M Li2SO4, DROPS - 3+3 micro-l, RESERVOIR - 42% MPEG-550, 0.1 M Li2SO4, 0.2 M imidazole malate, pH 5.5, CRYOSOLUTION - 18% ...Details: LCA-C134S-MTSEA at 3 mg/ml in 0.010 M Tris-HCl, pH 7.9, 0.050 M Li2SO4, DROPS - 3+3 micro-l, RESERVOIR - 42% MPEG-550, 0.1 M Li2SO4, 0.2 M imidazole malate, pH 5.5, CRYOSOLUTION - 18% MPEG2K, 22% MPD, 10% DMSO, 0.050 M bicine, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2009 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→50 Å / Num. all: 49624 / Num. obs: 49488 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 15.6 % / Biso Wilson estimate: 29.91 Å2 / Rmerge(I) obs: 0.147 / Rsym value: 0.143 / Net I/σ(I): 16.17 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: RIGID BODY Starting model: 4ELC Resolution: 1.697→39.937 Å / SU ML: 0.21 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): -3 / Phase error: 20.85 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.697→39.937 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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