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Yorodumi- PDB-7z60: Human transthyretin (TTR) complexed with Quercetin 3-O-beta-D-gal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z60 | ||||||
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Title | Human transthyretin (TTR) complexed with Quercetin 3-O-beta-D-galactoside | ||||||
Components | Transthyretin | ||||||
Keywords | PROTEIN TRANSPORT / Transthyretin / Thyroid hormone-binding protein / TTR-QUE-3GAL | ||||||
Function / homology | Function and homology information Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Ciccone, L. / Braca, A. / Orlandini, E. / Nencetti, S. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Crystals / Year: 2022 Title: Antioxidant Quercetin 3-O-Glycosylated Plant Flavonols Contribute to Transthyretin Stabilization Authors: Ciccone, L. / Tonali, N. / Fruchart-Gaillard, C. / Barlettani, L. / Rossello, A. / Braca, A. / Orlandini, E. / Nencetti, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z60.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z60.ent.gz | 49.8 KB | Display | PDB format |
PDBx/mmJSON format | 7z60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z60_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7z60_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7z60_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 7z60_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/7z60 ftp://data.pdbj.org/pub/pdb/validation_reports/z6/7z60 | HTTPS FTP |
-Related structure data
Related structure data | 4pmfS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13777.360 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02766 #2: Chemical | ChemComp-EDO / | #3: Chemical | ChemComp-J6O / | #4: Chemical | ChemComp-IMD / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.16 Å3/Da / Density % sol: 43.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Protein: 5 mg/ml TTR dialysed against 0.1 M NaCl, 0.05M Na acetate, pH 5.5. Precipitant:80% (30% PEG 4000, 0.2 M Imidazole Malate pH 6.0), 15% ((12% MPEG 5000, 0.1 Sodium Acetate pH 5.5) PH range: 5.5-6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 14, 2016 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→42.8 Å / Num. obs: 45603 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.99 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.4→1.43 Å / Num. unique obs: 90256 / CC1/2: 0.39 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PMF Resolution: 1.4→42.8 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.535 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.069 / 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: 104.95 Å2 / Biso mean: 27.601 Å2 / Biso min: 16.35 Å2
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Refinement step | Cycle: final / Resolution: 1.4→42.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.434 Å / Rfactor Rfree error: 0
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