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Open data
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Basic information
Entry | Database: PDB / ID: 7ovw | |||||||||
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Title | Binding domain of botulinum neurotoxin E in complex with GD1a | |||||||||
![]() | Neurotoxin type E | |||||||||
![]() | TOXIN / botulinum neurotoxin / ganglioside / toxin receptor / bacterial toxin / carbohydrate binding | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Masuyer, G. / Stenmark, P. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of Ganglioside Receptor Recognition by Botulinum Neurotoxin Serotype E. Authors: Masuyer, G. / Davies, J.R. / Stenmark, P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 344.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1021.9 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 32.6 KB | Display | |
Data in CIF | ![]() | 46.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ffzS 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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Unit cell |
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Components
#1: Protein | Mass: 54329.527 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Recombinant binding domain of botulinum neurotoxin E with N-terminal His and HA tags Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose | Source method: isolated from a genetically manipulated source #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.5 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.2 M sodium chloride 0.1 M phosphate/citrate pH 4.2, 20 % w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→53.77 Å / Num. obs: 44975 / % possible obs: 95.4 % / Redundancy: 3 % / Biso Wilson estimate: 34.8 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.066 / Rrim(I) all: 0.094 / Χ2: 0.88 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3757 / CC1/2: 0.807 / Rpim(I) all: 0.529 / Rrim(I) all: 0.748 / Χ2: 1.22 / % possible all: 92.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3FFZ Resolution: 2.2→53.77 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.9 / WRfactor Rfree: 0.272 / WRfactor Rwork: 0.218 / SU B: 8.149 / SU ML: 0.199 / Average fsc free: 0.8655 / Average fsc work: 0.8852 / Cross valid method: FREE R-VALUE / ESU R: 0.342 / ESU R Free: 0.25 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.213 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→53.77 Å
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Refine LS restraints |
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LS refinement shell |
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