+Open data
-Basic information
Entry | Database: PDB / ID: 3bta | ||||||
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Title | CRYSTAL STRUCTURE OF BOTULINUM NEUROTOXIN SEROTYPE A | ||||||
Components | PROTEIN (BOTULINUM NEUROTOXIN TYPE A) | ||||||
Keywords | TOXIN / NEUROTOXIN / ZINC PROTEASE / SUGAR BINDING PROTEIN / TRANSLOCATION | ||||||
Function / homology | Function and homology information host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 ...host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Clostridium botulinum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.2 Å | ||||||
Authors | Stevens, R.C. / Lacy, D.B. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Crystal structure of botulinum neurotoxin type A and implications for toxicity. Authors: Lacy, D.B. / Tepp, W. / Cohen, A.C. / DasGupta, B.R. / Stevens, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bta.cif.gz | 241.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bta.ent.gz | 194.9 KB | Display | PDB format |
PDBx/mmJSON format | 3bta.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bta_validation.pdf.gz | 429.9 KB | Display | wwPDB validaton report |
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Full document | 3bta_full_validation.pdf.gz | 509.7 KB | Display | |
Data in XML | 3bta_validation.xml.gz | 54.1 KB | Display | |
Data in CIF | 3bta_validation.cif.gz | 72.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/3bta ftp://data.pdbj.org/pub/pdb/validation_reports/bt/3bta | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 149479.812 Da / Num. of mol.: 1 / Fragment: FULL LENGTH TOXIN / Source method: isolated from a natural source / Source: (natural) Clostridium botulinum (bacteria) / Strain: HALL References: UniProt: P10845, UniProt: P0DPI1*PLUS, bontoxilysin |
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#2: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 4.5 Å3/Da / Density % sol: 70 % | ||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||
Crystal | *PLUS Density % sol: 70 % | ||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→20 Å / Num. obs: 40110 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 9 |
Reflection shell | Resolution: 3.3→3.4 Å / Redundancy: 4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3 / Rsym value: 0.28 / % possible all: 94.3 |
Reflection | *PLUS Num. measured all: 172169 / Rmerge(I) obs: 0.111 |
Reflection shell | *PLUS % possible obs: 94.3 % / Rmerge(I) obs: 0.483 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 3.2→20 Å / Data cutoff high rms absF: 1000000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
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Refinement step | Cycle: LAST / Resolution: 3.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.4 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.3 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.2 / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 3.3 Å / Lowest resolution: 3.4 Å / Rfactor Rfree: 0.3 / Rfactor Rwork: 0.23 |