+Open data
-Basic information
Entry | Database: PDB / ID: 1s0d | ||||||
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Title | Crystal structure of botulinum neurotoxin type B at pH 5.5 | ||||||
Components | Botulinum neurotoxin type B | ||||||
Keywords | Toxin / hydrolase / botulinum / neurotoxin / pH / metals | ||||||
Function / homology | Function and homology information 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 | Clostridium botulinum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Eswaramoorthy, S. / Kumaran, D. / Keller, J. / Swaminathan, S. | ||||||
Citation | Journal: Biochemistry / Year: 2004 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s0d.cif.gz | 283.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s0d.ent.gz | 225.3 KB | Display | PDB format |
PDBx/mmJSON format | 1s0d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s0/1s0d ftp://data.pdbj.org/pub/pdb/validation_reports/s0/1s0d | 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 (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: 150833.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Clostridium botulinum (bacteria) / Strain: type B / References: UniProt: P10844, bontoxilysin | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å |
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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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