+Open data
-Basic information
Entry | Database: PDB / ID: 5fw8 | ||||||
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Title | Structure of human transthyretin mutant E89K | ||||||
Components | TRANSTHYRETIN | ||||||
Keywords | TRANSPORT PROTEIN / T4-BINDING / T4-BINDING PROTEIN NON-AMYLOIDOGENIC | ||||||
Function / homology | Function and homology information Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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 / OTHER / Resolution: 1.6 Å | ||||||
Authors | Gallego, P. / Varejao, N. / Santanna, R. / Saraiva, M.J. / Ventura, S. / Reverter, D. | ||||||
Citation | Journal: To be Published Title: Structure of New Non-Amyloidogenic Mutant of Ttr A108V Authors: Gallego, P. / Varejao, N. / Santanna, R. / Saraiva, M.J. / Ventura, S. / Reverter, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fw8.cif.gz | 102.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fw8.ent.gz | 86.1 KB | Display | PDB format |
PDBx/mmJSON format | 5fw8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/5fw8 ftp://data.pdbj.org/pub/pdb/validation_reports/fw/5fw8 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13777.427 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02766 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.25 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979493 |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979493 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→42.41 Å / Num. obs: 31735 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 21.2 |
-Processing
Software | Name: REFMAC / Version: 5.5.0109 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.6→65.59 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.448 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.362 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→65.59 Å
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Refine LS restraints |
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