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- PDB-5vgx: Structure of the C. botulinum neurotoxin serotype A with Hg bound -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vgx | ||||||
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Title | Structure of the C. botulinum neurotoxin serotype A with Hg bound | ||||||
![]() | Botulinum neurotoxin type A | ||||||
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Function / homology | ![]() host cell junction / negative regulation of neurotransmitter secretion / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Carolan, J.P. / Allen, K.N. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189.5 KB | Display | ![]() |
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PDB format | ![]() | 148.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5vgvC ![]() 3bokS 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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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.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P10845, UniProt: P0DPI1*PLUS, ![]() |
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#2: Chemical | ChemComp-HG / ![]() |
#3: Chemical | ChemComp-ACT / ![]() |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.31 % |
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Crystal grow![]() | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG8000 8%, Calcium Acetate 0.2 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: ![]() ![]() ![]() |
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![]() |
Reflection | Resolution: 2.15→27.5393 Å / Num. obs: 22337 / % possible obs: 98 % / Redundancy: 4.8 % / Biso Wilson estimate: 24.46 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.1515 / Χ2: 1.084 / Net I/σ(I): 8.11 |
Reflection shell | Resolution: 2.15→2.227 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.3144 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2145 / CC1/2: 0.909 / Χ2: 0.371 / % possible all: 95 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3BOK Resolution: 2.15→27.537 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.81 Details: Refinement performed utilizing XYZ coordinate, real space, TLS, anomalous groups, and individual B-factor parameters.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→27.537 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: 5.1333 Å / Origin y: -0.583 Å / Origin z: 80.5388 Å
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Refinement TLS group | Selection details: all |