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Yorodumi- PDB-5v8u: Small Molecule Inhibitor ABS-143 Bound to the Botulinum Neurotoxi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5v8u | ||||||
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Title | Small Molecule Inhibitor ABS-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain | ||||||
Components | Botulinum neurotoxin type A | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / metalloprotease / drug design / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Allen, K.N. / Silvaggi, N.R. | ||||||
Citation | Journal: Toxicon / Year: 2017 Title: Small molecule metalloprotease inhibitor with in vitro, ex vivo and in vivo efficacy against botulinum neurotoxin serotype A. Authors: Jacobson, A.R. / Adler, M. / Silvaggi, N.R. / Allen, K.N. / Smith, G.M. / Fredenburg, R.A. / Stein, R.L. / Park, J.B. / Feng, X. / Shoemaker, C.B. / Deshpande, S.S. / Goodnough, M.C. / ...Authors: Jacobson, A.R. / Adler, M. / Silvaggi, N.R. / Allen, K.N. / Smith, G.M. / Fredenburg, R.A. / Stein, R.L. / Park, J.B. / Feng, X. / Shoemaker, C.B. / Deshpande, S.S. / Goodnough, M.C. / Malizio, C.J. / Johnson, E.A. / Pellett, S. / Tepp, W.H. / Tzipori, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5v8u.cif.gz | 467 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v8u.ent.gz | 388.9 KB | Display | PDB format |
PDBx/mmJSON format | 5v8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5v8u_validation.pdf.gz | 941.9 KB | Display | wwPDB validaton report |
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Full document | 5v8u_full_validation.pdf.gz | 970.5 KB | Display | |
Data in XML | 5v8u_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 5v8u_validation.cif.gz | 47.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/5v8u ftp://data.pdbj.org/pub/pdb/validation_reports/v8/5v8u | HTTPS FTP |
-Related structure data
Related structure data | 5v8pC 5v8rC 3bonS 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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Unit cell |
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-Components
#1: Protein | Mass: 50817.273 Da / Num. of mol.: 2 / Fragment: residues 1-424 / Mutation: P2Q 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): BL21(DE3) References: UniProt: P10845, UniProt: P0DPI1*PLUS, bontoxilysin #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.3 Å3/Da / Density % sol: 46.43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Mix equal volumes of 10-12 mg/ml enzyme (50 mM Na2HPO4, 2 mM EDTA, pH 6.5) and crystallization buffer (10-15% polyethylene glycol [PEG] 2,000 monomethyl ester, 0.2-0.3 M K2HPO4, 0.1 M D,L-malic acid pH 7.0) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 28, 2008 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 55823 / % possible obs: 95.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4395 / % possible all: 76.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BON Resolution: 2.05→37.563 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.58 / 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: 2.05→37.563 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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