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Yorodumi- PDB-4hjs: Kinetic stabilization of transthyretin through covalent modificat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hjs | ||||||
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Title | Kinetic stabilization of transthyretin through covalent modification of K15 by (E)-N-(4-(4-hydroxy-3,5-dimethylstyryl)ethanesulfonamide | ||||||
Components | Transthyretin | ||||||
Keywords | HORMONE BINDING PROTEIN / Thyroxine / retinol 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: 1.22 Å | ||||||
Authors | Connelly, S. / Wilson, I.A. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2013 Title: Stilbene vinyl sulfonamides as fluorogenic sensors of and traceless covalent kinetic stabilizers of transthyretin that prevent amyloidogenesis. Authors: Suh, E.H. / Liu, Y. / Connelly, S. / Genereux, J.C. / 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 | 4hjs.cif.gz | 117 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hjs.ent.gz | 90.7 KB | Display | PDB format |
PDBx/mmJSON format | 4hjs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hjs_validation.pdf.gz | 955.1 KB | Display | wwPDB validaton report |
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Full document | 4hjs_full_validation.pdf.gz | 962.6 KB | Display | |
Data in XML | 4hjs_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 4hjs_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/4hjs ftp://data.pdbj.org/pub/pdb/validation_reports/hj/4hjs | HTTPS FTP |
-Related structure data
Related structure data | 4hjtC 4hjuC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12703.217 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PALB, TTR / Plasmid: pmmHA / Production host: Escherichia coli (E. coli) / Strain (production host): Epicurean Gold / 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: 2.27 Å3/Da / Density % sol: 45.9 % |
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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 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2012 / 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→85.75 Å / Num. obs: 68549 / % possible obs: 97.9 % / Redundancy: 6 % / Rsym value: 0.086 / Χ2: 1.021 / Net I/σ(I): 61.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FBR Resolution: 1.22→85.75 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.2244 / WRfactor Rwork: 0.1923 / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.8285 / SU B: 1.511 / SU ML: 0.031 / SU R Cruickshank DPI: 0.0521 / SU Rfree: 0.0514 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.051 / 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: 210.21 Å2 / Biso mean: 22.4558 Å2 / Biso min: 8.21 Å2
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Refinement step | Cycle: LAST / Resolution: 1.22→85.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.221→1.253 Å / Total num. of bins used: 20
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