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Yorodumi- PDB-3aj5: HA1 (HA33) subcomponent of botulinum type C progenitor toxin comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aj5 | ||||||
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Title | HA1 (HA33) subcomponent of botulinum type C progenitor toxin complexed with N-acetylgalactosamine, bound at site II | ||||||
Components | Main hemagglutinin component | ||||||
Keywords | TOXIN / beta-trefoil / hemagglutinin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Clostridium botulinum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Nakamura, T. / Tonozuka, T. / Sato, R. / Oguma, K. / Nishikawa, A. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2011 Title: Molecular diversity of the two sugar-binding sites of the beta-trefoil lectin HA33/C (HA1) from Clostridium botulinum type C neurotoxin Authors: Nakamura, T. / Tonozuka, T. / Ito, S. / Takeda, Y. / Sato, R. / Matsuo, I. / Ito, Y. / Oguma, K. / Nishikawa, A. #1: Journal: J.Mol.Biol. / Year: 2008 Title: Sugar-binding sites of the HA1 subcomponent of Clostridium botulinum type C progenitor toxin Authors: Nakamura, T. / Tonozuka, T. / Ide, A. / Yuzawa, T. / Oguma, K. / Nishikawa, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aj5.cif.gz | 145.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aj5.ent.gz | 114 KB | Display | PDB format |
PDBx/mmJSON format | 3aj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3aj5_validation.pdf.gz | 449.9 KB | Display | wwPDB validaton report |
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Full document | 3aj5_full_validation.pdf.gz | 454.3 KB | Display | |
Data in XML | 3aj5_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 3aj5_validation.cif.gz | 46 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/3aj5 ftp://data.pdbj.org/pub/pdb/validation_reports/aj/3aj5 | HTTPS FTP |
-Related structure data
Related structure data | 3aj6C 3ah2S 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 33779.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (bacteria) / Strain: type C / Plasmid: pMAL-2X FLAG-HA1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P46084, UniProt: P0DPR0*PLUS #2: Sugar | #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: 2.54 Å3/Da / Density % sol: 51.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 12% ethanol, 1.7M sodium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 9, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 62088 / % possible obs: 98.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.8 / Num. unique all: 6068 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AH2 Resolution: 1.8→31 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / Cross valid method: THROUGHOUT / ESU R Free: 0.114 / 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: 18.23 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.799→1.846 Å / Total num. of bins used: 20
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