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- PDB-6zpd: gamma-tocopherol transfer protein -

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Basic information

Entry
Database: PDB / ID: 6zpd
Titlegamma-tocopherol transfer protein
ComponentsAlpha-tocopherol transfer protein
KeywordsLIPID TRANSPORT / SEC-14 like / vitamin E / nanoparticle / transcytosis
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
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
Similarity search - Domain/homology
Chem-VIV / Alpha-tocopherol transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsAeschimann, W. / Kammer, S. / Staats, S. / Stocker, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_156419 Switzerland
CitationJournal: Redox Biol / Year: 2020
Title: Engineering of a functional gamma-tocopherol transfer protein.
Authors: Aeschimann, W. / Kammer, S. / Staats, S. / Schneider, P. / Schneider, G. / Rimbach, G. / Cascella, M. / Stocker, A.
History
DepositionJul 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)27,6606
Polymers26,9401
Non-polymers7205
Water3,063170
1
A: Alpha-tocopherol transfer protein
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)663,837144
Polymers646,56124
Non-polymers17,276120
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area82890 Å2
ΔGint-1060 kcal/mol
Surface area218360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.687, 167.687, 167.687
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-305-

TRS

21A-305-

TRS

31A-527-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-tocopherol transfer protein / Alpha-TTP


Mass: 26940.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTPA, TPP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P49638

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Non-polymers , 5 types, 175 molecules

#2: 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.65 Å3/Da / Density % sol: 66.27 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 4000, ammonium sulfate, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0007 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0007 Å / Relative weight: 1
ReflectionResolution: 2.24→48.407 Å / Num. obs: 19658 / % possible obs: 99.8 % / Redundancy: 10.87 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 21.8
Reflection shellResolution: 2.24→2.38 Å / Redundancy: 10.92 % / Rmerge(I) obs: 0.686 / Num. unique obs: 3107 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OIP

1oip


Resolution: 2.24→48.407 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.85 / Phase error: 20.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2178 982 5 %
Rwork0.182 18675 -
obs0.1837 19657 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.84 Å2 / Biso mean: 45.953 Å2 / Biso min: 19.58 Å2
Refinement stepCycle: final / Resolution: 2.24→48.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 41 170 2115
Biso mean--44.69 53.35 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022028
X-RAY DIFFRACTIONf_angle_d0.6322742
X-RAY DIFFRACTIONf_chiral_restr0.026295
X-RAY DIFFRACTIONf_plane_restr0.003343
X-RAY DIFFRACTIONf_dihedral_angle_d12.427752
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.24-2.35770.26651370.235260899
2.3577-2.50540.25661380.22392626100
2.5054-2.69880.25151380.20472612100
2.6988-2.97040.22741390.20272640100
2.9704-3.40010.24571390.18272658100
3.4001-4.28340.18421420.16642694100
4.2834-6.660.20271490.16412837100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2635-0.0028-0.17840.49710.17070.1398-0.0052-0.29520.53980.27210.0301-0.31-0.4460.26890.00010.39640.0086-0.07930.3696-0.0370.409523.7191-34.808524.0831
20.03880.0401-0.01350.0444-0.03240.02320.6013-0.0602-0.33490.23490.67980.0692-0.5118-0.36180.0020.63980.14990.19520.723-0.08140.73457.72-37.631732.9196
30.6660.70370.18431.0078-0.37610.7496-0.0389-0.0610.01720.0930.0632-0.00990.0913-0.086200.22650.0912-0.01970.35040.01270.180617.0364-56.239829.8228
40.4565-0.42480.63130.9092-0.09180.9511-0.1806-0.16220.06330.0940.1170.0667-0.0475-0.002-00.24310.0456-0.00740.3716-0.00110.164815.3734-51.277229.0111
50.66430.27880.087-0.04680.45571.281-0.050.04160.0691-0.12480.03390.2265-0.1046-0.2927-00.21140.0548-0.03180.38530.03880.26596.1045-50.954922.4329
60.12780.1371-0.09030.2052-0.00960.0131-0.46430.29040.6383-0.73680.32990.4971-0.1961-0.5171-0.00070.36790.095-0.11060.53920.08370.43841.8251-45.702616.8267
70.7025-0.0057-0.16190.47380.4220.4498-0.05711.00430.3402-0.1539-0.26170.0435-0.0962-0.6901-0.19620.38490.0448-0.11670.57920.13830.279611.8785-46.786510.8905
80.01890.0640.09280.4010.16080.4919-0.06570.4946-0.4032-0.3515-0.0149-0.07550.71830.0876-0.00270.39730.0617-0.00810.4101-0.05050.322516.4232-65.888114.8498
90.4680.47120.40070.86670.73880.6912-0.1078-0.7188-0.0906-0.3261-0.2314-0.15490.40340.2493-0.09410.4560.2109-0.02720.3680.20440.319119.4453-66.287730.5979
100.2513-0.00950.00240.4469-0.08890.44630.0896-0.29780.2951-0.2215-0.1375-0.6018-0.29680.13450.01280.39510.0871-0.07180.47760.05220.233522.4799-48.910838.7856
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 48:75)A48 - 75
2X-RAY DIFFRACTION2(chain A and resid 76:83)A76 - 83
3X-RAY DIFFRACTION3(chain A and resid 84:120)A84 - 120
4X-RAY DIFFRACTION4(chain A and resid 121:158)A121 - 158
5X-RAY DIFFRACTION5(chain A and resid 159:203)A159 - 203
6X-RAY DIFFRACTION6(chain A and resid 204:215)A204 - 215
7X-RAY DIFFRACTION7(chain A and resid 216:223)A216 - 223
8X-RAY DIFFRACTION8(chain A and resid 224:250)A224 - 250
9X-RAY DIFFRACTION9(chain A and resid 251:258)A251 - 258
10X-RAY DIFFRACTION10(chain A and resid 259:278)A259 - 278

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