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Yorodumi- PDB-3esp: Human transthyretin (TTR) complexed with N-(3,5-Dibromo-4-hydroxy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3esp | ||||||
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Title | Human transthyretin (TTR) complexed with N-(3,5-Dibromo-4-hydroxyphenyl)-3,5-dimethyl-4-hydroxybenzamide | ||||||
Components | Transthyretin | ||||||
Keywords | HORMONE / Growth Factor / Amyloid / Disease mutation / Gamma-carboxyglutamic acid / Glycoprotein / Polymorphism / Polyneuropathy / Retinol-binding / Secreted / Thyroid hormone / Transport / Vitamin A | ||||||
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 / Resolution: 1.31 Å | ||||||
Authors | Connelly, S. / Wilson, I.A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2009 Title: Toward optimization of the second aryl substructure common to transthyretin amyloidogenesis inhibitors using biochemical and structural studies. Authors: Johnson, S.M. / Connelly, S. / 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 | 3esp.cif.gz | 115.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3esp.ent.gz | 90.4 KB | Display | PDB format |
PDBx/mmJSON format | 3esp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/3esp ftp://data.pdbj.org/pub/pdb/validation_reports/es/3esp | 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: 13777.360 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PALB, Transthyretin, 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: 2.12 Å3/Da / Density % sol: 41.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop 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: BL9-2 / Wavelength: 0.9795 Å |
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Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 1, 2007 Details: Flat mirror (vertical focusing), single crystal Si(111) bent monochromator (ho rizontal focusing) |
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: 1.31→64.28 Å / Num. obs: 55178 / % possible obs: 96.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 17.5 Å2 / Rsym value: 0.04 / Net I/σ(I): 36.6 |
Reflection shell | Resolution: 1.31→1.36 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.331 / % possible all: 75.1 |
-Processing
Software |
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Refinement | Resolution: 1.31→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.875 / SU B: 1.676 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.87 Å2 / Biso mean: 19.831 Å2 / Biso min: 9.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.31→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.31→1.345 Å / Total num. of bins used: 20
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