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Yorodumi- PDB-1oiz: The Molecular Basis of Vitamin E Retention: Structure of Human Al... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oiz | ||||||
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Title | The Molecular Basis of Vitamin E Retention: Structure of Human Alpha-Tocopherol Transfer Protein | ||||||
Components | ALPHA-TOCOPHEROL TRANSFER PROTEIN | ||||||
Keywords | TRANSPORT / ATAXIA / AVED / TRANSFER PROTEIN / TOCOPHEROL / VITAMIN E | ||||||
Function / homology | Function and homology information Vitamin E / vitamin E binding / vitamin E metabolic process / lipid transfer activity / vitamin transport / intermembrane lipid transfer / negative regulation of establishment of blood-brain barrier / positive regulation of amyloid-beta clearance / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol bisphosphate binding ...Vitamin E / vitamin E binding / vitamin E metabolic process / lipid transfer activity / vitamin transport / intermembrane lipid transfer / negative regulation of establishment of blood-brain barrier / positive regulation of amyloid-beta clearance / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol bisphosphate binding / embryonic placenta development / phosphatidylinositol-4,5-bisphosphate binding / lipid metabolic process / response to toxic substance / late endosome / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.88 Å | ||||||
Authors | Meier, R. / Tomizaki, T. / Schulze-Briese, C. / Baumann, U. / Stocker, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: The Molecular Basis of Vitamin E Retention: Structure of Human Alpha-Tocopherol Transfer Protein Authors: Meier, R. / Tomizaki, T. / Schulze-Briese, C. / Baumann, U. / Stocker, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oiz.cif.gz | 121.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oiz.ent.gz | 101.7 KB | Display | PDB format |
PDBx/mmJSON format | 1oiz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/1oiz ftp://data.pdbj.org/pub/pdb/validation_reports/oi/1oiz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Details | THE TWO MOLECULES IN THIS STRUCTURE HAVE TRT MOLECULESAT THE INTERFACE AND HAVE A BURIED SURFACE AREA OFOF 961.2 ANGSTROM**2 |
-Components
#1: Protein | Mass: 31791.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: CONTAINS CRAL_TRIO LIPID BINDING DOMAIN, RESIDUES 89-275 Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P49638 #2: Chemical | ChemComp-TRT / #3: Water | ChemComp-HOH / | Compound details | FUNCTION: BINDS ALPHA-TOCOPHEROL AND ENHANCES ITS TRANSFER BETWEEN SEPARATE MEMBRANES. DISEASE: ...FUNCTION: BINDS ALPHA-TOCOPHEROL | |
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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: 2.69 Å3/Da / Density % sol: 54.28 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: 5% PEG 6000, 0.1 M HEPES PH 7.5, 15% (V/V) MPD | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9791 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→30 Å / Num. obs: 54206 / % possible obs: 99.3 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.88→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 3.2 / % possible all: 93.1 |
Reflection | *PLUS Highest resolution: 1.88 Å / Lowest resolution: 30 Å / Num. measured all: 345927 / Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS % possible obs: 93.1 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 3.2 |
-Processing
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Refinement | Method to determine structure: OTHER / Resolution: 1.88→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.367 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 25.73 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→30 Å
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Refine LS restraints |
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