+Open data
-Basic information
Entry | Database: PDB / ID: 7fgk | ||||||
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Title | The Fab antibody single structure against tau protein. | ||||||
Components |
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Keywords | IMMUNE SYSTEM / tauopathies / tau protein / antibody / Alzheimer's disease / fab domain | ||||||
Function / homology | IODIDE ION Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Tsuchida, T. / Susa, K. / Kibiki, T. / Tsuchiya, T. / Miyamoto, K. / In, Y. / Minoura, K. / Taniguchi, T. / Ishida, T. / Tomoo, K. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: The free structure of the Fab domain of antibody that recognizes the PHF core region VQIINK in Tau protein. Authors: Tsuchida, T. / Susa, K. / Kibiki, T. / Tsuchiya, T. / Miyamoto, K. / In, Y. / Minoura, K. / Taniguchi, T. / Ishida, T. / Tomoo, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fgk.cif.gz | 106.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fgk.ent.gz | 79 KB | Display | PDB format |
PDBx/mmJSON format | 7fgk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fgk_validation.pdf.gz | 457.3 KB | Display | wwPDB validaton report |
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Full document | 7fgk_full_validation.pdf.gz | 465.7 KB | Display | |
Data in XML | 7fgk_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 7fgk_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/7fgk ftp://data.pdbj.org/pub/pdb/validation_reports/fg/7fgk | HTTPS FTP |
-Related structure data
Related structure data | 4hk3S 5eorS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23229.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) | ||||||
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#2: Antibody | Mass: 23531.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 20% PEG 3350, 15% Glycerol, 0.1M Ammonium iodide, 10mM Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5406 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: May 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 2→27.82 Å / Num. obs: 22009 / % possible obs: 99.6 % / Redundancy: 3.62 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.458 / Num. unique obs: 22009 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HK3, 5EOR Resolution: 2.3→27.82 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.903 / SU B: 10.52 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.286 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.789 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→27.82 Å
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Refine LS restraints |
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