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Yorodumi- PDB-1y1d: Crystal structure of transthyretin in complex with iododiflunisal -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y1d | ||||||
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Title | Crystal structure of transthyretin in complex with iododiflunisal | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / Transthyretin / Amyloid / Iododiflunisal | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Gales, L. / Macedo-Ribeiro, S. / Arsequell, G. / Valencia, G. / Saraiva, M.J. / Damas, A.M. | ||||||
Citation | Journal: Biochem.J. / Year: 2005 Title: Human transthyretin in complex with iododiflunisal: structural features associated with a potent amyloid inhibitor. Authors: Gales, L. / Macedo-Ribeiro, S. / Arsequell, G. / Valencia, G. / Saraiva, M.J. / Damas, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y1d.cif.gz | 62.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y1d.ent.gz | 44.5 KB | Display | PDB format |
PDBx/mmJSON format | 1y1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y1d_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1y1d_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1y1d_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 1y1d_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/1y1d ftp://data.pdbj.org/pub/pdb/validation_reports/y1/1y1d | HTTPS FTP |
-Related structure data
Related structure data | 1f86S S: Starting model for refinement |
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Similar structure data |
-Links
-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: 13777.360 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Plasmid: pHNTR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02766 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.18 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.2M sodium citrate, 2.4M ammonium sulfate, 6% glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 4, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→85.844 Å / Num. all: 26953 / Num. obs: 26934 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.102 / Rsym value: 0.088 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 4.5 / Num. unique all: 3638 / Rsym value: 0.174 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID: 1F86 Resolution: 1.7→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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