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Yorodumi- PDB-5vgv: Structure of the C. botulinum neurotoxin serotype A with Cu bound -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vgv | ||||||
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Title | Structure of the C. botulinum neurotoxin serotype A with Cu bound | ||||||
Components | Botulinum neurotoxin type A | ||||||
Keywords | TOXIN / botulinum / neurotoxin / metalloprotease | ||||||
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: 2.6 Å | ||||||
Authors | Carolan, J.P. / Allen, K.N. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2017 Title: Metal Ions Effectively Ablate the Action of Botulinum Neurotoxin A. Authors: Bremer, P.T. / Pellett, S. / Carolan, J.P. / Tepp, W.H. / Eubanks, L.M. / Allen, K.N. / Johnson, E.A. / Janda, K.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vgv.cif.gz | 183.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vgv.ent.gz | 143.5 KB | Display | PDB format |
PDBx/mmJSON format | 5vgv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/5vgv ftp://data.pdbj.org/pub/pdb/validation_reports/vg/5vgv | HTTPS FTP |
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-Related structure data
Related structure data | 5vgxC 3bokS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 50602.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Polyhistidine-tagged botulinum neurotoxin A light chain Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botA, atx, bna / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P10845, UniProt: P0DPI1*PLUS, bontoxilysin | ||||
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#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.83 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG8000 6%, Calcium Acetate 0.1 M, Sodium Cacodylate 0.1 M |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: N2 Stream |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.36994 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2017 / Details: Mirror: Rh coated flat, toroidal focusing |
Radiation | Monochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.36994 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→31.965 Å / Num. obs: 12795 / % possible obs: 97 % / Redundancy: 7.5 % / CC1/2: 0.98 / Rmerge(I) obs: 0.1658 / Χ2: 1.508 / Net I/σ(I): 12.32 |
Reflection shell | Resolution: 2.6→2.693 Å / Redundancy: 5 % / Rmerge(I) obs: 0.3537 / Mean I/σ(I) obs: 3.92 / Num. unique obs: 1221 / CC1/2: 0.889 / Χ2: 0.679 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BOK Resolution: 2.6→31.965 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 28.8 / 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: 2.6→31.965 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 15.1941 Å / Origin y: -0.5173 Å / Origin z: 16.1268 Å
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Refinement TLS group | Selection details: all |