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- PDB-1oip: The Molecular Basis of Vitamin E Retention: Structure of Human Al... -

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Basic information

Entry
Database: PDB / ID: 1oip
TitleThe Molecular Basis of Vitamin E Retention: Structure of Human Alpha-Tocopherol Transfer Protein
ComponentsALPHA-TOCOPHEROL TRANSFER PROTEIN
KeywordsTRANSPORT / ATAXIA / AVED / TRANSFER PROTEIN / TOCOPHEROL / VITAMIN E TRANSPORT / DISEASE MUTATION
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
Alpha-tocopherol transfer / N-terminal domain of phosphatidylinositol transfer protein sec14p / Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. ...Alpha-tocopherol transfer / N-terminal domain of phosphatidylinositol transfer protein sec14p / Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Helicase, Ruva Protein; domain 3 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-VIV / Alpha-tocopherol transfer protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMeier, R. / Tomizaki, T. / Schulze-Briese, C. / Baumann, U. / Stocker, A.
CitationJournal: 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
DepositionJun 24, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-TOCOPHEROL TRANSFER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4144
Polymers31,7921
Non-polymers6233
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)77.810, 77.810, 128.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein ALPHA-TOCOPHEROL TRANSFER PROTEIN / ALPHA-TTP / TTPA / TPP1


Mass: 31791.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-VIV / (2R)-2,5,7,8-TETRAMETHYL-2-[(4R,8R)-4,8,12-TRIMETHYLTRIDECYL]CHROMAN-6-OL


Mass: 430.706 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H50O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: BINDS ALPHA-TOCOPHEROL AND ENHANCES ITS TRANSFER BETWEEN SEPARATE MEMBRANES. DISEASE: ...FUNCTION: BINDS ALPHA-TOCOPHEROL AND ENHANCES ITS TRANSFER BETWEEN SEPARATE MEMBRANES. DISEASE: DEFECTS IN TTPA ARE THE CAUSE OF ATAXIA WITH ISOLATED VITAMIN E DEFICIENCY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growpH: 5.6 / Details: 12% PEG 6000, 0.1 M NA-CITRATE PH 5.6, 0.1 M LISO4
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 5.6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
212 %(w/v)PEG60001reservoir
30.1 Msodium citrate1reservoirpH5.6
40.1 M1reservoirLiSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.1407
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1407 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 29375 / % possible obs: 99.7 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 22.8
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 3.5 / % possible all: 97.7
Reflection
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 20 Å / Num. measured all: 317025 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 97.7 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.54 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.875 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1472 5 %RANDOM
Rwork0.19 ---
obs0.192 27963 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2---0.29 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2047 0 41 125 2213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212142
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2611.9712905
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8585250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021602
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2580.2977
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9272.51256
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.8822.52036
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3473886
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7113.5869
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.273 102
Rwork0.243 1955
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.3

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