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- PDB-7z5s: Crystal Structure of botulinum neurotoxin A2 cell binding domain ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7z5s | ||||||
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Title | Crystal Structure of botulinum neurotoxin A2 cell binding domain in complex with GD1a | ||||||
![]() | Botulinum neurotoxin | ||||||
![]() | TOXIN / ganglioside / neurotoxin / botulinum / receptor / GD1a | ||||||
Function / homology | ![]() negative regulation of neurotransmitter secretion / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / proteolysis / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gregory, K.S. / Acharya, K.R. / Liu, S.M. / Mahadeva, T.B. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural Features of Clostridium botulinum Neurotoxin Subtype A2 Cell Binding Domain. Authors: Gregory, K.S. / Mahadeva, T.B. / Liu, S.M. / Acharya, K.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 | ![]() | 193.7 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 34 KB | Display | |
Data in CIF | ![]() | 48.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7z5tC ![]() 5moyS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 50416.266 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source 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)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: 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: 3.63 Å3/Da / Density % sol: 66.1 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M Lithium citrate tribasic tetrahydrate 20 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→105.07 Å / Num. obs: 83782 / % possible obs: 100 % / Redundancy: 27.3 % / CC1/2: 0.99 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 21.9 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4633 / CC1/2: 0.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5MOY Resolution: 2.1→105.068 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.194 / WRfactor Rwork: 0.159 / Average fsc free: 0.8683 / Average fsc work: 0.8793 / Cross valid method: FREE R-VALUE / ESU R: 0.151 / ESU R Free: 0.145 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: 46.052 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→105.068 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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