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Yorodumi- PDB-5akt: Transthyretin binding heterogeneity and anti-amyloidogenic activi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5akt | ||||||
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Title | Transthyretin binding heterogeneity and anti-amyloidogenic activity of natural polyphenols and their metabolites: resveratrol-4'-O- glucuronide | ||||||
Components | TRANSTHYRETIN | ||||||
Keywords | TRANSPORT PROTEIN / AMYLOID / FIBRILLOGENESIS / FIBRILLOGENESIS INHIBITORS / POLYPHENOLS / POLYPHENOL METABOLITES / NEGATIVE COOPERATIVITY | ||||||
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: 1.35 Å | ||||||
Authors | Florio, P. / Folli, C. / Cianci, M. / Del Rio, D. / Zanotti, G. / Berni, R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Transthyretin Binding Heterogeneity and Anti-Amyloidogenic Activity of Natural Polyphenols and Their Metabolites Authors: Florio, P. / Folli, C. / Cianci, M. / Del Rio, D. / Zanotti, G. / Berni, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5akt.cif.gz | 72.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5akt.ent.gz | 56.5 KB | Display | PDB format |
PDBx/mmJSON format | 5akt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5akt_validation.pdf.gz | 977.1 KB | Display | wwPDB validaton report |
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Full document | 5akt_full_validation.pdf.gz | 980.8 KB | Display | |
Data in XML | 5akt_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 5akt_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/5akt ftp://data.pdbj.org/pub/pdb/validation_reports/ak/5akt | HTTPS FTP |
-Related structure data
Related structure data | 5aksC 5akvC 5al0C 5al8C 5cr1C 1f41S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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 / Fragment: UNP RESIDUES 21-147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET11B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02766 #2: Chemical | #3: Chemical | #4: 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: 2.31 Å3/Da / Density % sol: 46.76 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: CRYSTALS OF WT HUMAN TTR- LIGAND COMPLEXES WERE OBTAINED AT ROOM TEMPERATURE IN ABOUT ONE WEEK BY CO-CRYSTALLIZATION, USING THE HANGING-DROP VAPOR DIFFUSION METHOD. THE PROTEIN (5 MG/ML), IN ...Details: CRYSTALS OF WT HUMAN TTR- LIGAND COMPLEXES WERE OBTAINED AT ROOM TEMPERATURE IN ABOUT ONE WEEK BY CO-CRYSTALLIZATION, USING THE HANGING-DROP VAPOR DIFFUSION METHOD. THE PROTEIN (5 MG/ML), IN 20 MM SODIUM PHOSPHATE, PH 7, WAS INCUBATED WITH A FOUR-FOLD MOLAR EXCESS OF LIGANDS SOLUBILIZED IN DMSO. DROPS WERE FORMED BY MIXING EQUAL VOLUMES OF THE SOLUTION CONTAINING LIGAND-TTR COMPLEXES AND OF THE RESERVOIR/PRECIPITANT SOLUTION (2.2 M AMMONIUM SULPHATE, 0.1 M KCL, 0.03 M SODIUM PHOSPHATE, PH 7.0). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.967 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 31, 2013 / Details: KB MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.967 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→63.67 Å / Num. obs: 51577 / % possible obs: 99.3 % / Observed criterion σ(I): 3.4 / Redundancy: 6.4 % / Biso Wilson estimate: 15.55 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.4 / % possible all: 99.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1F41 Resolution: 1.35→63.672 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 18.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→63.672 Å
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Refine LS restraints |
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LS refinement shell |
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