+Open data
-Basic information
Entry | Database: PDB / ID: 6zvm | ||||||
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Title | Botulinum neurotoxin B2 binding domain in complex with GD1a | ||||||
Components | Neurotoxin | ||||||
Keywords | TOXIN / botulinum neurotoxin / ganglioside / gd1a / bont / b2 | ||||||
Function / homology | Function and homology information negative regulation of neurotransmitter secretion / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / proteolysis / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Clostridium botulinum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Davies, J.R. / Masuyer, G. / Stenmark, P. | ||||||
Citation | Journal: Toxins / Year: 2020 Title: Structural and Biochemical Characterization of Botulinum Neurotoxin Subtype B2 Binding to Its Receptors. Authors: Davies, J.R. / Masuyer, G. / Stenmark, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zvm.cif.gz | 119.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zvm.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6zvm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/6zvm ftp://data.pdbj.org/pub/pdb/validation_reports/zv/6zvm | HTTPS FTP |
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-Related structure data
Related structure data | 6zvnC 4kbbS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 52464.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: bontb / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8GR96 | ||||
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#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-(1-4)-beta-D-glucopyranose | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.97 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.16 M calcium acetate hydrate, 0.08 M MES pH 6.5, 14.4% (w/v) PEG 8000, 20% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→63.816 Å / Num. obs: 46758 / % possible obs: 99.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 16.98 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.042 / Rrim(I) all: 0.109 / Χ2: 0.96 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2663 / CC1/2: 0.682 / Rpim(I) all: 0.356 / Rrim(I) all: 0.777 / Χ2: 1 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4kbb Resolution: 1.8→63.73 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: FREE R-VALUE / ESU R: 0.114 / ESU R Free: 0.112 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.469 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→63.73 Å
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Refine LS restraints |
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LS refinement shell |
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