+Open data
-Basic information
Entry | Database: PDB / ID: 4pmf | ||||||
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Title | Human transthyretin (TTR) complexed with curcumin | ||||||
Components | Transthyretin | ||||||
Keywords | Thyroid hormone-binding protein / Human transthyretin (TTR) complex / hydrophobic ligand solubilization. | ||||||
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: 1.35 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 | 4pmf.cif.gz | 75.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pmf.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 4pmf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pmf_validation.pdf.gz | 941.8 KB | Display | wwPDB validaton report |
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Full document | 4pmf_full_validation.pdf.gz | 950.2 KB | Display | |
Data in XML | 4pmf_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 4pmf_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/4pmf ftp://data.pdbj.org/pub/pdb/validation_reports/pm/4pmf | HTTPS FTP |
-Related structure data
Related structure data | 4pm1SC 4pmeC 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: 12832.396 Da / Num. of mol.: 2 / Fragment: UNP residues 29-146 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: SERUM / Tissue: SERUM / References: UniProt: P02766 #2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Precipitant: 40% MPEG 2,000, 1% dioxane, 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. ...Details: Precipitant: 40% MPEG 2,000, 1% dioxane, 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 5K, 0.1 M mixed (sodium acetate, ADA, bicine 20% pH 4 and 80% pH 9), 3 milli-M Curcumin for 20 min PH range: 8.2 / 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: 0.9793 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: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→39 Å / Num. all: 53047 / Num. obs: 52995 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.95 % / Biso Wilson estimate: 16.55 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.061 / Net I/σ(I): 18.07 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 9.03 % / Mean I/σ(I) obs: 1.94 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PM1 Resolution: 1.35→39 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.21 / 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: 1.35→39 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / % reflection Rfree: 5 % / % reflection obs: 100 %
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