+Open data
-Basic information
Entry | Database: PDB / ID: 6mhj | ||||||||||||
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Title | Structure of BoNT mutant | ||||||||||||
Components | Botulinum neurotoxin type A | ||||||||||||
Keywords | TOXIN / Protein translocation / Botulinum neurotoxin | ||||||||||||
Function / homology | Function and homology information Toxicity of botulinum toxin type A (botA) / ganglioside GT1b binding / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane ...Toxicity of botulinum toxin type A (botA) / ganglioside GT1b binding / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane Similarity search - Function | ||||||||||||
Biological species | Clostridium botulinum A str. ATCC 19397 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.019 Å | ||||||||||||
Authors | Lam, K. / Jin, R. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2018 Title: A viral-fusion-peptide-like molecular switch drives membrane insertion of botulinum neurotoxin A1. Authors: Lam, K.H. / Guo, Z. / Krez, N. / Matsui, T. / Perry, K. / Weisemann, J. / Rummel, A. / Bowen, M.E. / Jin, R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mhj.cif.gz | 147.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mhj.ent.gz | 116.6 KB | Display | PDB format |
PDBx/mmJSON format | 6mhj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/6mhj ftp://data.pdbj.org/pub/pdb/validation_reports/mh/6mhj | HTTPS FTP |
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-Related structure data
Related structure data | 6dkkC 3v0aS 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
#1: Protein | Mass: 37485.676 Da / Num. of mol.: 1 / Mutation: F658E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum A str. ATCC 19397 (bacteria) Gene: botA, atx, bonT / Production host: Escherichia coli (E. coli) / References: UniProt: P0DPI0, bontoxilysin |
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#2: Chemical | ChemComp-PO4 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.98 Å3/Da / Density % sol: 79.43 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 2.4 M ammonium phosphate, 0.1 M Tris pH 8.5, 0.05 % n-dodecyl beta-D-maltoside |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.12709 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12709 Å / Relative weight: 1 |
Reflection | Resolution: 3.02→42.87 Å / Num. obs: 18540 / % possible obs: 99.9 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 15 |
Reflection shell | Resolution: 3.02→3.2 Å / Rmerge(I) obs: 0.616 / Num. unique obs: 2932 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3V0A Resolution: 3.019→42.87 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.66 / 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: 3.019→42.87 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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