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- PDB-7uia: Crystal structure of BoNT/E receptor binding domain in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7uia | ||||||
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Title | Crystal structure of BoNT/E receptor binding domain in complex with SV2 and VHH | ||||||
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![]() | TOXIN / toxin-receptor complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, Z. / Jin, R. / Chen, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for botulinum neurotoxin E recognition of synaptic vesicle protein 2. Authors: Liu, Z. / Lee, P.G. / Krez, N. / Lam, K.H. / Liu, H. / Przykopanski, A. / Chen, P. / Yao, G. / Zhang, S. / Tremblay, J.M. / Perry, K. / Shoemaker, C.B. / Rummel, A. / Dong, M. / Jin, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 271.7 KB | Display | ![]() |
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PDB format | ![]() | 214.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 45.9 KB | Display | |
Data in CIF | ![]() | 63.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7uibC ![]() 7uieC ![]() 3ffzS ![]() 5jlvS ![]() 6glwS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 4 molecules CFDA
#2: Protein | Mass: 12198.499 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others) #3: Protein | Mass: 47392.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Antibody , 1 types, 2 molecules BE
#1: Antibody | Mass: 14390.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others) |
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-Sugars , 2 types, 8 molecules ![](data/chem/img/NAG.gif)
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 167 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-PEG / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.91 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES, pH 7.5, 0.2 M potassium sulfate, 20% PEG 3350, and 5% (v/v) PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→137.16 Å / Num. obs: 52103 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.999 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 2.59→2.67 Å / Num. unique obs: 4444 / CC1/2: 0.894 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3FFZ, 5JLV, 6GLW Resolution: 2.59→109.01 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.9 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 0.711 / ESU R Free: 0.303 / 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: 51.741 Å2
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Refinement step | Cycle: 1 / Resolution: 2.59→109.01 Å
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Refine LS restraints |
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