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Yorodumi- PDB-6r67: Crystal structure of transthyretin in complex with CHF5075, a flu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r67 | ||||||
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Title | Crystal structure of transthyretin in complex with CHF5075, a flurbiprofen analogue | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / Amyloidosis / tetramer / binding protein | ||||||
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: 1.3 Å | ||||||
Authors | Loconte, V. / Menozzi, I. / Ferrari, A. / Berni, R. / Zanotti, G. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2019 Title: Structure-activity relationships of flurbiprofen analogues as stabilizers of the amyloidogenic protein transthyretin. Authors: Loconte, V. / Menozzi, I. / Ferrari, A. / Folli, C. / Imbimbo, B.P. / Zanotti, G. / Berni, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r67.cif.gz | 67.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r67.ent.gz | 49.8 KB | Display | PDB format |
PDBx/mmJSON format | 6r67.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/6r67 ftp://data.pdbj.org/pub/pdb/validation_reports/r6/6r67 | HTTPS FTP |
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-Related 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: 15904.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / 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: 1.81 Å3/Da / Density % sol: 31.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.2 M ammonium sulfate, 0.1M KCl, 30 mM sodium phosphate, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.95372 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→42.32 Å / Num. obs: 57493 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.3 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.034 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.818 / Mean I/σ(I) obs: 4 / Num. unique obs: 2817 / Rpim(I) all: 0.359 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→37.91 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.771 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.054 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.987 Å2
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Refinement step | Cycle: 1 / Resolution: 1.3→37.91 Å
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Refine LS restraints |
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