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- PDB-3c88: 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: 3c88 | ||||||
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Title | Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with inhibitory peptide RRGC | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / Botulinum Neurotoxin type A / catalytic domain / endopeptidase / Bio-warfare agent / Protease / Secreted / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Kumaran, D. / Swaminathan, S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.6 KB | Display | ![]() |
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PDB format | ![]() | 80.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3bwiSC ![]() 3c89C ![]() 3c8aC ![]() 3c8bC S: Starting model for refinement C: citing same article ( |
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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 / Protein/peptide , 2 types, 2 molecules AB
#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.) ![]() ![]() ![]() ![]() References: UniProt: A5HZZ9, UniProt: P0DPI1*PLUS, bontoxilysin |
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#2: Protein/peptide | Mass: 490.605 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 4 types, 348 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / | ||||
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#4: Chemical | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 12% PEG 3350, 0.2M ammonium sulfate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 51491 / Num. obs: 51491 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 1.6→1.65 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.127 / Mean I/σ(I) obs: 3 / Num. unique all: 2938 / % possible all: 63 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3BWI Resolution: 1.6→32.04 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 124600.31 / 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: 38.4111 Å2 / ksol: 0.358906 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→32.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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