+Open data
-Basic information
Entry | Database: PDB / ID: 3win | ||||||
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Title | Clostridium botulinum Hemagglutinin | ||||||
Components |
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Keywords | TOXIN / bacterial pathogenesis / bacterial toxins / carbohydrate-binding protein / E-cadherin / epithelial cell / protein complexes / botulinum toxin / hemagglutinin / Beta-trefoil | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Clostridium botulinum B (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Amatsu, S. / Sugawara, Y. / Matsumura, T. / Fujinaga, Y. / Kitadokoro, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Crystal Structure of Clostridium botulinum Whole Hemagglutinin Reveals a Huge Triskelion-shaped Molecular Complex Authors: Amatsu, S. / Sugawara, Y. / Matsumura, T. / Kitadokoro, K. / Fujinaga, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3win.cif.gz | 542.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3win.ent.gz | 451.9 KB | Display | PDB format |
PDBx/mmJSON format | 3win.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3win_validation.pdf.gz | 481.7 KB | Display | wwPDB validaton report |
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Full document | 3win_full_validation.pdf.gz | 540.3 KB | Display | |
Data in XML | 3win_validation.xml.gz | 51.7 KB | Display | |
Data in CIF | 3win_validation.cif.gz | 70.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/3win ftp://data.pdbj.org/pub/pdb/validation_reports/wi/3win | HTTPS FTP |
-Related structure data
Related structure data | 2e4mS 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: 22295.070 Da / Num. of mol.: 1 / Fragment: UNP residues 7-294 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum B (bacteria) / Gene: ha3 / Plasmid: pET52b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q33CP8 | ||
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#2: Protein | Mass: 48761.977 Da / Num. of mol.: 1 / Fragment: UNP residues 2-146 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum B (bacteria) / Gene: ha3 / Plasmid: pET52b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q33CP8 | ||
#3: Protein | Mass: 19248.541 Da / Num. of mol.: 1 / Fragment: UNP residues 19-188 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum B (bacteria) / Gene: hem17/B, ha2 / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q45841 | ||
#4: Protein | Mass: 36059.090 Da / Num. of mol.: 2 / Fragment: UNP residues 196-626 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum B (bacteria) / Gene: ha1 / Plasmid: pET52b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q33CP6 #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: 5.51 Å3/Da / Density % sol: 77.67 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.25M ammonium chloride, 3%(w/v) polyethylene glycol 4000, 3% trehalose, 3%(w/v) benzamidine HCl, 3%(w/v) methylpentanediol, 3%(w/v) ethylene glycol, 0.1M calcium chloride, 0.1M Tris-HCl , ...Details: 0.25M ammonium chloride, 3%(w/v) polyethylene glycol 4000, 3% trehalose, 3%(w/v) benzamidine HCl, 3%(w/v) methylpentanediol, 3%(w/v) ethylene glycol, 0.1M calcium chloride, 0.1M Tris-HCl , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jul 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 45595 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 83.2 Å2 / Rmerge(I) obs: 0.054 |
Reflection shell | Resolution: 3.5→3.63 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.494 / Num. unique all: 4478 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2E4M Resolution: 3.5→48.43 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.867 / SU B: 41.489 / SU ML: 0.295 / Cross valid method: THROUGHOUT / ESU R: 2.112 / ESU R Free: 0.444 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 113.213 Å2
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Refinement step | Cycle: LAST / Resolution: 3.5→48.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.59 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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