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- PDB-4i89: Crystal structure of transthyretin in complex with diflunisal at ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4i89 | ||||||
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Title | Crystal structure of transthyretin in complex with diflunisal at acidic pH | ||||||
![]() | Transthyretin | ||||||
![]() | transport protein/inhibitor / amyloidosis / fibrillogenesis inhibitor / transthyretin stabilizers / T4 or T3 hormone / plasma / transport protein-inhibitor complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Zanotti, G. / Cendron, L. / Folli, C. / Florio, P. / Imbimbo, B.P. / Berni, R. | ||||||
![]() | ![]() Title: Structural evidence for native state stabilization of a conformationally labile amyloidogenic transthyretin variant by fibrillogenesis inhibitors. Authors: Zanotti, G. / Cendron, L. / Folli, C. / Florio, P. / Imbimbo, B.P. / Berni, R. #1: ![]() Title: Acidic pH-induced conformational changes in amyloidogenic mutant transthyretin. Authors: Pasquato, N. / Berni, R. / Folli, C. / Alfieri, B. / Cendron, L. / Zanotti, G. #2: ![]() Title: Amyloidogenic potential of transthyretin variants: insights from structural and computational analyses. Authors: Cendron, L. / Trovato, A. / Seno, F. / Folli, C. / Alfieri, B. / Zanotti, G. / Berni, 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 | ![]() | 47.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 20.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4i85C ![]() 4i87SC C: citing same article ( S: Starting model for refinement |
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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: 13751.280 Da / Num. of mol.: 2 / Fragment: Transthyretin (unp residues 21-147) / Mutation: I84S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.99 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 15% (w/v) PEG 2000 monomethylether, 0.1 M ammonium sulfate, 0.05 M sodium acetate buffer, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 30, 2010 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→32.93 Å / Num. all: 27383 / Num. obs: 27383 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.69→1.78 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 5.2 / Num. unique all: 3948 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4I87 Resolution: 1.69→32.93 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 19.42 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.731 Å2 / ksol: 0.374 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.69→32.93 Å
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Refine LS restraints |
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LS refinement shell |
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