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Open data
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Basic information
Entry | Database: PDB / ID: 1s0d | ||||||
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Title | Crystal structure of botulinum neurotoxin type B at pH 5.5 | ||||||
![]() | Botulinum neurotoxin type B | ||||||
![]() | Toxin / hydrolase / botulinum / neurotoxin / pH / metals | ||||||
Function / homology | ![]() Toxicity of botulinum toxin type B (botB) / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding / host cell plasma membrane ...Toxicity of botulinum toxin type B (botB) / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Eswaramoorthy, S. / Kumaran, D. / Keller, J. / Swaminathan, S. | ||||||
![]() | ![]() Title: Role of metals in the biological activity of Clostridium botulinum neurotoxins Authors: Eswaramoorthy, S. / Kumaran, D. / Keller, J. / Swaminathan, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 283.8 KB | Display | ![]() |
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PDB format | ![]() | 225.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1s0bC ![]() 1s0cC ![]() 1s0eC ![]() 1s0fC ![]() 1s0gC ![]() 1epwS 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: 150833.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.79 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: PEG 4000, MES, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Method: vapor diffusionDetails: Swaminathan, S., (2000) Acta Crystallogr., Sect.D, 56, 1024. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: BRANDEIS - B1.2 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 78587 / Num. obs: 78587 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.397 / Num. unique all: 6230 / % possible all: 74.8 |
Reflection | *PLUS Num. measured all: 275095 |
Reflection shell | *PLUS % possible obs: 74.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EPW Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 2 % / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.223 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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