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Yorodumi- PDB-4qrf: Crystal structure of V30M mutant human transthyretin complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qrf | ||||||
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Title | Crystal structure of V30M mutant human transthyretin complexed with caffeic acid phenethyl ester | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / transporter / thyroxine binding | ||||||
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: 1.8 Å | ||||||
Authors | Yokoyama, T. / Kosaka, Y. / Mizuguchi, M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Inhibitory Activities of Propolis and Its Promising Component, Caffeic Acid Phenethyl Ester, against Amyloidogenesis of Human Transthyretin Authors: Yokoyama, T. / Kosaka, Y. / Mizuguchi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qrf.cif.gz | 61 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qrf.ent.gz | 43.7 KB | Display | PDB format |
PDBx/mmJSON format | 4qrf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qrf_validation.pdf.gz | 959.6 KB | Display | wwPDB validaton report |
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Full document | 4qrf_full_validation.pdf.gz | 961.7 KB | Display | |
Data in XML | 4qrf_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 4qrf_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/4qrf ftp://data.pdbj.org/pub/pdb/validation_reports/qr/4qrf | HTTPS FTP |
-Related structure data
Related structure data | 4pweC 4pwfC 4pwgC 4pwhC 4pwiC 4pwjC 4pwkC 4pewS 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: 17342.582 Da / Num. of mol.: 2 / Mutation: V30M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): M30 / 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: 1.69 Å3/Da / Density % sol: 27.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10-30% PEG400, 0.1M HEPES, 0.2M CaCl2, 1mM caffeic acid phenethyl ester, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 13, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→50 Å / Num. all: 22978 / Num. obs: 22978 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 26.39 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 1.3 / Num. unique all: 1082 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PEW Resolution: 1.8→32.888 Å / FOM work R set: 0.812 / SU ML: 0.25 / σ(F): 1.38 / Phase error: 25.57 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.16 Å2 / Biso mean: 25.38 Å2 / Biso min: 8.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→32.888 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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