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Yorodumi- PDB-4fi8: Kinetic Stabilization of transthyretin through covalent modificat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fi8 | ||||||
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Title | Kinetic Stabilization of transthyretin through covalent modification of K15 by 4-bromo-3-(5-(3,5-dichloro-4-hydroxyphenyl)-1,3,4-oxadiazol-2-yl)-benzenesulfonamide | ||||||
Components | Transthyretin | ||||||
Keywords | HORMONE/HORMONE INHIBITOR / hormone / binding protein / Covalent kinetic stabilizer / HORMONE-HORMONE INHIBITOR 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å | ||||||
Authors | Connelly, S. / Grimster, N. / Wilson, I.A. / Kelly, J.W. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2013 Title: Aromatic Sulfonyl Fluorides Covalently Kinetically Stabilize Transthyretin to Prevent Amyloidogenesis while Affording a Fluorescent Conjugate. Authors: Grimster, N.P. / Connelly, S. / Baranczak, A. / Dong, J. / Krasnova, L.B. / Sharpless, K.B. / Powers, E.T. / Wilson, I.A. / Kelly, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fi8.cif.gz | 117.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fi8.ent.gz | 91.4 KB | Display | PDB format |
PDBx/mmJSON format | 4fi8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fi8_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4fi8_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4fi8_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 4fi8_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/4fi8 ftp://data.pdbj.org/pub/pdb/validation_reports/fi/4fi8 | HTTPS FTP |
-Related structure data
Related structure data | 4fi6C 4fi7C 2fbrS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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: PMMHA / Production host: Escherichia coli (E. coli) / Strain (production host): Epicurian Gold / References: UniProt: P02766 #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | 0UC UNDERGOES NUCLEOPHIL | |
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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: 2.15 Å3/Da / Density % sol: 42.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: The wt-TTR was concentrated to 4 mg/ml in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature with inhibitors using the vapor-diffusion sitting drop method, crystals ...Details: The wt-TTR was concentrated to 4 mg/ml in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature with inhibitors using the vapor-diffusion sitting drop method, crystals were grown from 1.395 M sodium citrate, 3.5% v/v glycerol at ph 5.5. The crystals were frozen using a cryo-protectant solution of 1.395 m sodium citrate, ph 5.5, containing 10% v/v glycerol, vapor diffusion, sitting drop, temperature 298.0, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2011 / Details: Rh coated flat mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.22→86.143 Å / Num. obs: 70853 / % possible obs: 99.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 16.9 Å2 / Rsym value: 0.079 / Χ2: 0.815 / Net I/σ(I): 10.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FBR Resolution: 1.22→86.14 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.2026 / WRfactor Rwork: 0.1715 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.9059 / SU B: 1.082 / SU ML: 0.022 / SU R Cruickshank DPI: 0.0443 / SU Rfree: 0.0438 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 94.08 Å2 / Biso mean: 21.2477 Å2 / Biso min: 11.38 Å2
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Refinement step | Cycle: LAST / Resolution: 1.22→86.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.22→1.252 Å / Total num. of bins used: 20
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