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Yorodumi- PDB-3w68: Crystal structure of mouse alpha-tocopherol transfer protein in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w68 | ||||||
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Title | Crystal structure of mouse alpha-tocopherol transfer protein in complex with alpha-tocopherol and phosphatidylinositol-(4,5)-bisphosphate | ||||||
Components | Alpha-tocopherol transfer protein | ||||||
Keywords | TRANSPORT PROTEIN / Ataxia / Vitamin E deficiency / AVED / Transfer protein / Tocopherol / Vitamin E / Disease mutation / alpha-tocopherol transfer / alpha-tocopherol / phosphatidyl inositol phosphates | ||||||
Function / homology | Function and homology information Vitamin E / vitamin E binding / intracellular pH reduction / vitamin E metabolic process / vitamin binding / lipid transfer activity / vitamin transport / intermembrane lipid transfer / negative regulation of establishment of blood-brain barrier / negative regulation of epithelial cell apoptotic process ...Vitamin E / vitamin E binding / intracellular pH reduction / vitamin E metabolic process / vitamin binding / lipid transfer activity / vitamin transport / intermembrane lipid transfer / negative regulation of establishment of blood-brain barrier / negative regulation of epithelial cell apoptotic process / positive regulation of amyloid-beta clearance / phosphatidylinositol-3,4-bisphosphate binding / response to pH / phosphatidylinositol bisphosphate binding / embryonic placenta development / phosphatidylinositol-4,5-bisphosphate binding / placenta development / response to toxic substance / late endosome / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Ohto, U. / Satow, Y. | ||||||
Citation | Journal: Science / Year: 2013 Title: Impaired alpha-TTP-PIPs interaction underlies familial vitamin E deficiency Authors: Kono, N. / Ohto, U. / Hiramatsu, T. / Urabe, M. / Uchida, Y. / Satow, Y. / Arai, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w68.cif.gz | 437.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w68.ent.gz | 362.8 KB | Display | PDB format |
PDBx/mmJSON format | 3w68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/3w68 ftp://data.pdbj.org/pub/pdb/validation_reports/w6/3w68 | HTTPS FTP |
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-Related structure data
Related structure data | 3w67C 1r5lS 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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2 |
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5 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 30624.289 Da / Num. of mol.: 4 / Fragment: UNP residues 21-275 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ttpa / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8BWP5 |
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-Non-polymers , 5 types, 259 molecules
#2: Chemical | ChemComp-VIV / ( #3: Chemical | #4: Chemical | ChemComp-PBU / ( | #5: Chemical | ChemComp-PO4 / #6: 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: 2.57 Å3/Da / Density % sol: 52.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 4-7%(w/v) PEG3350, 15%(w/v) MPD, 85mM NaCl, 85mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 26, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30 Å / Num. obs: 75088 / Rsym value: 0.065 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1R5L Resolution: 2.05→29.32 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.132 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.17 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.365 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→29.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.099 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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