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Yorodumi- PDB-4pme: Human transthyretin (TTR) complexed with ferulic acid and curcumin. -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pme | ||||||
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Title | Human transthyretin (TTR) complexed with ferulic acid and curcumin. | ||||||
Components | Transthyretin | ||||||
Keywords | Thyroid hormone-binding protein / Human transthyretin (TTR) complexes / solubilization of hydrophobic ligands / curcumin degradation | ||||||
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: 1.264 Å | ||||||
Authors | Stura, E.A. / Ciccone, L. | ||||||
Citation | Journal: N Biotechnol / Year: 2014 Title: Transthyretin complexes with curcumin and bromo-estradiol: evaluation of solubilizing multicomponent mixtures. Authors: Ciccone, L. / Tepshi, L. / Nencetti, S. / Stura, E.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pme.cif.gz | 79.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pme.ent.gz | 58.9 KB | Display | PDB format |
PDBx/mmJSON format | 4pme.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pme_validation.pdf.gz | 707.6 KB | Display | wwPDB validaton report |
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Full document | 4pme_full_validation.pdf.gz | 713.9 KB | Display | |
Data in XML | 4pme_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 4pme_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/4pme ftp://data.pdbj.org/pub/pdb/validation_reports/pm/4pme | HTTPS FTP |
-Related structure data
Related structure data | 4pm1SC 4pmfC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 12961.576 Da / Num. of mol.: 2 / Fragment: UNP residues 29-145 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02766 |
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-Non-polymers , 5 types, 283 molecules
#2: Chemical | ChemComp-CUR / ( | ||
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#3: Chemical | ChemComp-NA / | ||
#4: Chemical | ChemComp-EDO / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: protein: 5 mg/ml dialysed in 0.1 M NaCl, 0.05 M NaAc, pH 5.5 with 5 milli-M curcumin. precipitant:: 45% MPEG 2,000, 0.1 M sodium cacodylate, pH 7.5. Cryoprotectant: 40% mixed (25% dioxane, ...Details: protein: 5 mg/ml dialysed in 0.1 M NaCl, 0.05 M NaAc, pH 5.5 with 5 milli-M curcumin. precipitant:: 45% MPEG 2,000, 0.1 M sodium cacodylate, pH 7.5. Cryoprotectant: 40% mixed (25% dioxane, 25% DMSO, 12.5% ethylene glycol, 12.5% 1,2-propanediol, 12.5% glycerol, 12.5% 2,3-butanediol), 50% (25% MPEG 5000, 0.1 M mixed (Na acetate, ADA, Bicine buffer: 40% pH 4.0 / 60% pH 9.0) PH range: 7.0-7.5 / Temp details: cooled incubator |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryostream |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979338 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2014 / Details: bent cylindrical mirror |
Radiation | Monochromator: horizontally diffracting Si (111) monochromator and Pt coated mirrors in Kirkpatrick-Baez geometry for focusing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979338 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→42.335 Å / Num. all: 63275 / Num. obs: 63061 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.84 % / Biso Wilson estimate: 18.24 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.052 / Net I/σ(I): 18.58 |
Reflection shell | Resolution: 1.26→1.34 Å / Redundancy: 8.53 % / Mean I/σ(I) obs: 1.02 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PM1 Resolution: 1.264→42.335 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.41 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.264→42.335 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / % reflection Rfree: 5 %
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