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- PDB-7ybr: Crystal structure of human transthyretin variant A97S complexed w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ybr | ||||||
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Title | Crystal structure of human transthyretin variant A97S complexed with Tolcapone | ||||||
![]() | Transthyretin | ||||||
![]() | TRANSPORT PROTEIN / Transport thyroxine | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, Y.S. / Huang, C.H. / Tzeng, S.R. | ||||||
Funding support | 1items
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64 KB | Display | ![]() |
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PDB format | ![]() | 44.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 934.4 KB | Display | ![]() |
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Full document | ![]() | 935 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 16.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7y6jC ![]() 7ycqC ![]() 8hy4C ![]() 2qgbS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 14995.710 Da / Num. of mol.: 2 / Mutation: A97S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 37.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG 400, 200 mM Calcium Chloride, 100 mM HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→30 Å / Num. obs: 31836 / % possible obs: 99.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 17.67 Å2 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.024 / Rrim(I) all: 0.049 / Net I/σ(I): 31.57377 |
Reflection shell | Resolution: 1.71→1.77 Å / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 3 / Num. unique obs: 2555 / Rpim(I) all: 0.211 / Rrim(I) all: 0.425 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2QGB Resolution: 1.71→25.87 Å / SU ML: 0.184 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.4889 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: 22.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→25.87 Å
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Refine LS restraints |
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LS refinement shell |
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