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Yorodumi- PDB-3n7j: Crystal structure of botulinum neurotoxin serotype D binding domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n7j | ||||||
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Title | Crystal structure of botulinum neurotoxin serotype D binding domain | ||||||
Components | Botulinum neurotoxin type D | ||||||
Keywords | TOXIN / Botulinum Neurotoxin / HCR/D / Ganglioside Binding Loop | ||||||
Function / homology | Function and homology information Toxicity of botulinum toxin type D (botD) / ganglioside GT1b binding / bontoxilysin / 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Fu, Z. / Baldwin, M.R. / Karalewitz, A. / Kroken, A. / Barbieri, J.T. / Kim, J.-J.P. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Identification of a Unique Ganglioside Binding Loop within Botulinum Neurotoxins C and D-SA . Authors: Karalewitz, A.P. / Kroken, A.R. / Fu, Z. / Baldwin, M.R. / Kim, J.J. / Barbieri, J.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n7j.cif.gz | 99.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n7j.ent.gz | 74.8 KB | Display | PDB format |
PDBx/mmJSON format | 3n7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/3n7j ftp://data.pdbj.org/pub/pdb/validation_reports/n7/3n7j | HTTPS FTP |
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-Related structure data
Related structure data | 3n7kC 3n7lC 3n7mC 3fuoS C: citing same article (ref.) S: Starting model for refinement |
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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: 48237.254 Da / Num. of mol.: 1 / Fragment: Receptor Binding Domain (UNP Residues 862-1276) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botD, Clostridium phage d-16 phi / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19321 |
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#2: 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: 55.8 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Hepes pH 7.5, 10% PEG8000, 8% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 3, 2008 / Details: mirrors |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.8 Å / Num. obs: 35231 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Biso Wilson estimate: 26.4 Å2 / Rsym value: 0.09 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 2793 / Rsym value: 0.497 / % possible all: 77.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FUO Resolution: 2→29.8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 78983.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.8734 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 42.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→29.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.03 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 20
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Xplor file |
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