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- PDB-5bqn: Crystal structure of the LHn fragment of botulinum neurotoxin typ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5bqn | ||||||
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Title | Crystal structure of the LHn fragment of botulinum neurotoxin type D, mutant H233Y E230Q | ||||||
![]() | Botulinum neurotoxin type D,Botulinum neurotoxin type D | ||||||
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Function / homology | ![]() Toxicity of botulinum toxin type D (botD) / ganglioside GT1b binding / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Masuyer, G. / Davies, J.R. / Moore, K. / Chaddock, J.A. / Acharya, K.R. | ||||||
![]() | ![]() Title: Structural analysis of Clostridium botulinum neurotoxin type D as a platform for the development of targeted secretion inhibitors. Authors: Masuyer, G. / Davies, J.R. / Moore, K. / Chaddock, J.A. / Ravi Acharya, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 356.2 KB | Display | ![]() |
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PDB format | ![]() | 291.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5bqmC ![]() 2fpqS 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
#1: Protein | Mass: 101855.594 Da / Num. of mol.: 1 Mutation: H233Y, E230Q,H233Y, E230Q,H233Y, E230Q,H233Y, E230Q Source method: isolated from a genetically manipulated source Details: Engineered fragment of the botulinum neurotoxin type D with inactive catalytic domain and translocation domain. An engineered linker region is present between the two domains. Residues 442- ...Details: Engineered fragment of the botulinum neurotoxin type D with inactive catalytic domain and translocation domain. An engineered linker region is present between the two domains. Residues 442-457, 494-510, 872-884 were disordered. Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-EPE / ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.8 Å3/Da / Density % sol: 74.6 % |
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Crystal grow![]() | Temperature: 289.1 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30 % v/v pentaerythritol ethoxylate (15/4 EO/OH), 0.1 M HEPES 7.5, 6 % w/v polyvinylpyrrolidone |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→150 Å / Num. all: 86306 / Num. obs: 86306 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 2.6 % / Rmerge(I) obs: 1.09 / Mean I/σ(I) obs: 0.5 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2FPQ Resolution: 2.3→150 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 22.239 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.043 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→150 Å
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Refine LS restraints |
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