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- PDB-1r5l: Crystal Structure of Human Alpha-Tocopherol Transfer Protein Boun... -

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Basic information

Entry
Database: PDB / ID: 1r5l
TitleCrystal Structure of Human Alpha-Tocopherol Transfer Protein Bound to its Ligand
ComponentsPROTEIN (Alpha-tocopherol transfer protein)
KeywordsTRANSPORT PROTEIN / ATTP / TOCOPHEROL / ATAXIA WITH VITAMIN E DEFICIENCY
Function / homology
Function and homology information


Vitamin E / vitamin E binding / vitamin E metabolic process / lipid transfer activity / vitamin transport / negative regulation of establishment of blood-brain barrier / intermembrane lipid transfer / 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 / negative regulation of establishment of blood-brain barrier / intermembrane lipid transfer / 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 / MAD / Resolution: 1.5 Å
AuthorsMin, K.C. / Kovall, R.A. / Hendrickson, W.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal structure of human alpha-tocopherol transfer protein bound to its ligand: Implications for ataxia with vitamin E deficiency
Authors: Min, K.C. / Kovall, R.A. / Hendrickson, W.A.
History
DepositionOct 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (Alpha-tocopherol transfer protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7492
Polymers30,3181
Non-polymers4311
Water4,558253
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.096, 77.151, 85.397
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (Alpha-tocopherol transfer protein) / Alpha-TTP


Mass: 30318.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTPA OR TPP1 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P49638
#2: Chemical ChemComp-VIV / (2R)-2,5,7,8-TETRAMETHYL-2-[(4R,8R)-4,8,12-TRIMETHYLTRIDECYL]CHROMAN-6-OL / Α-Tocopherol


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


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 37.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: PEG 4000, TRIS base, sodium chloride, pH 8.10, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / PH range low: 8.4 / PH range high: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 mMPMSF1drop
25 mg/mlprotein1drop
35 %(w/v)PEG40001reservoir
4100 mMTris-HCl1reservoirpH8.0-8.4

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONNSLS X4A10.99180.9818
SYNCHROTRONNSLS X4A20.9792,0.9789,0.9686
Detector
TypeIDDetectorDate
ADSC QUANTUM 4r1CCDJun 20, 2003
ADSC QUANTUM 42CCDApr 20, 2003
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.99181
20.98181
30.97921
40.97891
50.96861
ReflectionResolution: 1.5→50 Å / Num. obs: 79802 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 21.9 Å2 / Rsym value: 0.074 / Net I/σ(I): 24.5
Reflection shellResolution: 1.5→1.55 Å / Mean I/σ(I) obs: 8.4 / Num. unique all: 6558 / Rsym value: 0.213 / % possible all: 89.2
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 50 Å / Num. measured all: 325760 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 89.2 % / Rmerge(I) obs: 0.213

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
ARP/wARPmodel building
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.5→37.36 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 208546.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.213 7829 9.8 %RANDOM
Rwork0.187 ---
obs0.187 79802 97.2 %-
all-81965 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.376 Å2 / ksol: 0.35932 e/Å3
Displacement parametersBiso mean: 25 Å2
Baniso -1Baniso -2Baniso -3
1-5.06 Å20 Å20 Å2
2---2.92 Å20 Å2
3----2.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.5→37.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2111 0 31 253 2395
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d1.25
X-RAY DIFFRACTIONc_mcbond_it2.141.5
X-RAY DIFFRACTIONc_mcangle_it2.872
LS refinement shellResolution: 1.5→1.55 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.252 749 10.3 %
Rwork0.235 6558 -
obs--89.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2XDICT.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMXDICT.TOP
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0154
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.25

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