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- PDB-8awi: Crystal structure of Human Transthyretin at 1.15 Angstrom resolution -
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Open data
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Basic information
Entry | Database: PDB / ID: 8awi | ||||||
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Title | Crystal structure of Human Transthyretin at 1.15 Angstrom resolution | ||||||
![]() | Transthyretin | ||||||
![]() | TRANSPORT PROTEIN / Transthyretin / hormone-binding protein / thyroxine / transport / fluorescence / amyloid | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Derbyshire, D.J. / Hammarstrom, P. / von Castelmur, E. / Begum, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Transthyretin Binding Mode Dichotomy of Fluorescent trans -Stilbene Ligands. Authors: Begum, A. / Zhang, J. / Derbyshire, D. / Wu, X. / Konradsson, P. / Hammarstrom, P. / von Castelmur, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.1 KB | Display | ![]() |
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PDB format | ![]() | 88.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.4 KB | Display | ![]() |
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Full document | ![]() | 431.9 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7q9lC ![]() 7q9nC ![]() 7q9oC C: citing same article ( |
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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: 13090.689 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Evidence for alternative conformation(s) for loop A:100-103 at crystal packing interface. Density not convincing enough to model with full occupancy. Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: protein at 5.2mg/ml in 10mM sodium phosphate pH7.6 and 100mM potassium chloride was mixed 1:1 with 1.3-1.6M sodium citrate and 3.5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97993 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→64.325 Å / Num. obs: 84053 / % possible obs: 98.8 % / Redundancy: 23.1 % / CC1/2: 0.996 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.15→1.17 Å / Num. unique obs: 39058 / CC1/2: 0.67 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: in-house model Resolution: 1.15→64.325 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 107.83 Å2 / Biso mean: 20.7441 Å2 / Biso min: 11.46 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→64.325 Å
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