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Yorodumi- PDB-1dvy: CRYSTAL STRUCTURE OF TRANSTHYRETIN IN COMPLEX WITH N-(M-TRIFLUORO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dvy | ||||||
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Title | CRYSTAL STRUCTURE OF TRANSTHYRETIN IN COMPLEX WITH N-(M-TRIFLUOROMETHYLPHENYL) PHENOXAZINE-4,6-DICARBOXYLIC ACID | ||||||
Components | TRANSTHYRETIN | ||||||
Keywords | HORMONE/GROWTH FACTOR / THYROXINE TRANSPORT / SIGNALING PROTEIN / HORMONE-GROWTH FACTOR COMPLEX | ||||||
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 / Resolution: 1.9 Å | ||||||
Authors | Klabunde, T. / Petrassi, H.M. / Oza, V.B. / Kelly, J.W. / Sacchettini, J.C. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2000 Title: Rational design of potent human transthyretin amyloid disease inhibitors. Authors: Klabunde, T. / Petrassi, H.M. / Oza, V.B. / Raman, P. / Kelly, J.W. / Sacchettini, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dvy.cif.gz | 57.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dvy.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dvy_validation.pdf.gz | 519 KB | Display | wwPDB validaton report |
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Full document | 1dvy_full_validation.pdf.gz | 521.5 KB | Display | |
Data in XML | 1dvy_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | 1dvy_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/1dvy ftp://data.pdbj.org/pub/pdb/validation_reports/dv/1dvy | HTTPS FTP |
-Related structure data
Related structure data | 1dvqC 1dvsC 1dvtC 1dvuC 1dvxC 1dvzC C: citing same article (ref.) |
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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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Details | The biological assembly is a tetramer constructed from the homodimer (chain A and B) and a symmetry mate generated by the two-fold |
-Components
#1: Protein | Mass: 13420.968 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P02766 #2: Chemical | ChemComp-BPD / | #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: 2.26 Å3/Da / Density % sol: 45.61 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: potassium chloride, potassium phosphate, ammonium sulfate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Nov 11, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→10 Å / Num. all: 22052 / Num. obs: 22052 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.43 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.173 / % possible all: 97.5 |
Reflection | *PLUS Lowest resolution: 10 Å / Num. measured all: 75643 |
Reflection shell | *PLUS % possible obs: 97.5 % |
-Processing
Software |
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Refinement | Resolution: 1.9→8 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber Details: The structure contains two PHENOX molecules that bind in each of two independent binding sites of the tetramer. Since the binding is along the 2-fold crystallographic axis, an occupancy of 0. ...Details: The structure contains two PHENOX molecules that bind in each of two independent binding sites of the tetramer. Since the binding is along the 2-fold crystallographic axis, an occupancy of 0.5 corresponds to saturation of each of the binding sites.
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Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 8 Å / σ(F): 3 / % reflection Rfree: 10 % / Rfactor obs: 0.202 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |