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Yorodumi- PDB-1f31: CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN B COMPLEXED... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f31 | |||||||||
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Title | CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN B COMPLEXED WITH A TRISACCHARIDE | |||||||||
Components | BOTULINUM NEUROTOXIN TYPE B | |||||||||
Keywords | TOXIN / botulinum / zinc / metalloprotease / transmembrane / neurotoxin / complex / ganglioside | |||||||||
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 / Resolution: 2.6 Å | |||||||||
Authors | Swaminathan, S. / Eswaramoorthy, S. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2000 Title: Structural analysis of the catalytic and binding sites of Clostridium botulinum neurotoxin B. Authors: Swaminathan, S. / Eswaramoorthy, S. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallization and Preliminary X-ray Analysis of Clostridium botulinum Neurotoxin Type B Authors: Swaminathan, S. / Eswaramoorthy, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f31.cif.gz | 274.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f31.ent.gz | 215.3 KB | Display | PDB format |
PDBx/mmJSON format | 1f31.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f31_validation.pdf.gz | 471 KB | Display | wwPDB validaton report |
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Full document | 1f31_full_validation.pdf.gz | 496.1 KB | Display | |
Data in XML | 1f31_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 1f31_validation.cif.gz | 43.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/1f31 ftp://data.pdbj.org/pub/pdb/validation_reports/f3/1f31 | HTTPS FTP |
-Related structure data
Related structure data | 1epwSC 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) / References: UniProt: P10844, bontoxilysin |
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#2: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-alpha-D-galactopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-SO4 / |
#5: 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: 2.75 Å3/Da / Density % sol: 55 % | |||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: PEG 4000, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K | |||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||
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: X25 / Wavelength: 1.1 |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Apr 21, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 47458 / Num. obs: 47458 / % possible obs: 67 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.052 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.34 / % possible all: 12.9 |
Reflection | *PLUS |
-Processing
Software |
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Refinement | Starting model: 1EPW Resolution: 2.6→50 Å / Cross valid method: FREE-R / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 50 Å / σ(F): 2 / % reflection Rfree: 4 % / Rfactor all: 0.214 / Rfactor obs: 0.21 / Rfactor Rfree: 0.27 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 19.3 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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