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- PDB-4tlk: Crystal Structure of Human Transthyretin Ser85Pro/Glu92Pro Mutant -
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Open data
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Basic information
Entry | Database: PDB / ID: 4tlk | ||||||
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Title | Crystal Structure of Human Transthyretin Ser85Pro/Glu92Pro Mutant | ||||||
![]() | Transthyretin | ||||||
![]() | TRANSPORT PROTEIN / human transthyretin / amyloid / transthyretin / mutant | ||||||
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 | ![]() ![]() | ||||||
![]() | Saelices, L. / Cascio, D. / Sawaya, M. / Eisenberg, D.S. | ||||||
![]() | ![]() Title: Uncovering the Mechanism of Aggregation of Human Transthyretin. Authors: Saelices, L. / Johnson, L.M. / Liang, W.Y. / Sawaya, M.R. / Cascio, D. / Ruchala, P. / Whitelegge, J. / Jiang, L. / Riek, R. / Eisenberg, D.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.6 KB | Display | ![]() |
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PDB format | ![]() | 79.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.8 KB | Display | ![]() |
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Full document | ![]() | 449 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4tkwC ![]() 4tl4C ![]() 4tl5C ![]() 4tlsC ![]() 4tltC ![]() 4tm9C ![]() 4tneC ![]() 4xfnC ![]() 4xfoC C: citing same article ( |
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Similar structure data |
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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: 13897.609 Da / Num. of mol.: 2 / Fragment: UNP residues 29-147 / Mutation: S85P, E92P Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% (W/V) PEG-1000, 0.1M Imidazole, 0.2M Calcium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2013 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→63.38 Å / Num. obs: 48638 / % possible obs: 99 % / Redundancy: 6.7 % / Biso Wilson estimate: 21.48 Å2 / Net I/σ(I): 13.34 |
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Processing
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Refinement | Resolution: 1.44→63.38 Å / Cor.coef. Fo:Fc: 0.9578 / Cor.coef. Fo:Fc free: 0.9526 / SU R Cruickshank DPI: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.065 / SU Rfree Blow DPI: 0.062 / SU Rfree Cruickshank DPI: 0.062
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Displacement parameters | Biso max: 126.13 Å2 / Biso mean: 25.51 Å2 / Biso min: 13.12 Å2
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Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.44→63.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.44→1.48 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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