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Yorodumi- PDB-7ycq: Crystal structure of human transthyretin variant A97S complexed w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ycq | ||||||
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Title | Crystal structure of human transthyretin variant A97S complexed with Diflunisal | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / Transport thyroxine | ||||||
Function / homology | Function and homology information Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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: 1.99 Å | ||||||
Authors | Wang, Y.S. / Huang, C.H. / Tzeng, S.R. | ||||||
Funding support | 1items
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Citation | Journal: Protein Sci. / Year: 2023 Title: A molecular basis for tetramer destabilization and aggregation of transthyretin Ala97Ser. Authors: Wang, Y.S. / Huang, C.H. / Liou, G.G. / Hsueh, H.W. / Liang, C.T. / Tseng, H.C. / Huang, S.J. / Chao, C.C. / Hsieh, S.T. / Tzeng, S.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ycq.cif.gz | 107.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ycq.ent.gz | 80.5 KB | Display | PDB format |
PDBx/mmJSON format | 7ycq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/7ycq ftp://data.pdbj.org/pub/pdb/validation_reports/yc/7ycq | HTTPS FTP |
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-Related structure data
Related structure data | 7y6jC 7ybrC 8hy4C 2qgbS S: Starting model for refinement C: citing same article (ref.) |
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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: Protein | Mass: 13793.360 Da / Num. of mol.: 2 / Mutation: A97S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766 #2: Chemical | #3: 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: 2.11 Å3/Da / Density % sol: 41.75 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.5 M Ammonium Sulfate, 0.01M citrate buffer; soaked with 800 micromolar Dilfunisal |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.989→30 Å / Num. obs: 16347 / % possible obs: 99 % / Redundancy: 6.2 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.024 / Rrim(I) all: 0.061 / Net I/σ(I): 28.268292682927 |
Reflection shell | Resolution: 1.99→2.06 Å / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3.5081967213115 / Num. unique obs: 1581 / CC1/2: 0.941 / CC star: 0.985 / Rpim(I) all: 0.195 / Rrim(I) all: 0.445 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QGB Resolution: 1.99→22.26 Å / SU ML: 0.1895 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2858 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.04 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→22.26 Å
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Refine LS restraints |
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LS refinement shell |
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