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Yorodumi- PDB-7fgr: The cross-reaction complex structure with VQIFNK peptide and the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7fgr | ||||||
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Title | The cross-reaction complex structure with VQIFNK peptide and the tau antibody's Fab domain. | ||||||
Components |
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Keywords | IMMUNE SYSTEM / tauopathies / tau protein / antibody / Alzheimer's disease / Fab domain | ||||||
Function / homology | IODIDE ION / AMMONIUM ION Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Tsuchida, 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 cross-reaction complex structure with VQIFNK peptide and the tau antibody's Fab domain. Authors: Tsuchida, 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 | 7fgr.cif.gz | 107.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fgr.ent.gz | 79.7 KB | Display | PDB format |
PDBx/mmJSON format | 7fgr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fgr_validation.pdf.gz | 464.9 KB | Display | wwPDB validaton report |
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Full document | 7fgr_full_validation.pdf.gz | 471.6 KB | Display | |
Data in XML | 7fgr_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 7fgr_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/7fgr ftp://data.pdbj.org/pub/pdb/validation_reports/fg/7fgr | HTTPS FTP |
-Related structure data
Related structure data | 6lraS 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
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 748.889 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-Antibody , 2 types, 2 molecules HL
#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: 23402.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
-Non-polymers , 5 types, 339 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-IOD / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.76 Å3/Da / Density % sol: 55.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 18% PEG 3350, 20% Glycerol, 0.2M 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: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Mar 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→32.67 Å / Num. obs: 23945 / % possible obs: 95.7 % / Redundancy: 3.64 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.84 / Num. unique obs: 23945 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LRA Resolution: 2.2→32.67 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.649 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.284 / ESU R Free: 0.239 / 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: 45.662 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→32.67 Å
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Refine LS restraints |
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