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Yorodumi- PDB-5b2h: Crystal structure of HA33 from Clostridium botulinum serotype C s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b2h | ||||||
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Title | Crystal structure of HA33 from Clostridium botulinum serotype C strain Yoichi | ||||||
Components | HA-33 | ||||||
Keywords | SUGAR BINDING PROTEIN / Hemagglutinin | ||||||
Function / homology | Function and homology information Ricin-type beta-trefoil lectin domain-like / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Clostridium botulinum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Akiyama, T. / Hayashi, S. / Matsumoto, T. / Hasegawa, K. / Yamano, A. / Suzuki, T. / Niwa, K. / Watanabe, T. / Sagane, Y. / Yajima, S. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2016 Title: Conformational divergence in the HA-33/HA-17 trimer of serotype C and D botulinum toxin complex Authors: Sagane, Y. / Hayashi, S. / Akiyama, T. / Matsumoto, T. / Hasegawa, K. / Yamano, A. / Suzuki, T. / Niwa, K. / Watanabe, T. / Yajima, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b2h.cif.gz | 133.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b2h.ent.gz | 102.9 KB | Display | PDB format |
PDBx/mmJSON format | 5b2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5b2h_validation.pdf.gz | 439.3 KB | Display | wwPDB validaton report |
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Full document | 5b2h_full_validation.pdf.gz | 441.9 KB | Display | |
Data in XML | 5b2h_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 5b2h_validation.cif.gz | 35.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/5b2h ftp://data.pdbj.org/pub/pdb/validation_reports/b2/5b2h | 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: 32846.363 Da / Num. of mol.: 2 / Fragment: UNP residues 3-285 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (bacteria) / Strain: C-Yoichi / Gene: ha-33 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93HT5 #2: Chemical | ChemComp-PGE / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris-HCl, 5% PEG400, 8% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 95 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 9, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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. obs: 48719 / % possible obs: 100 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.062 / Rrim(I) all: 0.106 / Χ2: 1.388 / Net I/av σ(I): 15.477 / Net I/σ(I): 8.8 / Num. measured all: 141410 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2E4M Resolution: 2.2→30.7 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.715 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.36 Å2 / Biso mean: 33.575 Å2 / Biso min: 14.21 Å2
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Refinement step | Cycle: final / Resolution: 2.2→30.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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