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- PDB-1ln1: Crystal Structure of Human Phosphatidylcholine Transfer Protein i... -

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Basic information

Entry
Database: PDB / ID: 1ln1
TitleCrystal Structure of Human Phosphatidylcholine Transfer Protein in Complex with Dilinoleoylphosphatidylcholine
ComponentsPhosphatidylcholine transfer protein
KeywordsLIPID BINDING PROTEIN / START Domain
Function / homology
Function and homology information


phosphatidylcholine transporter activity / Mitochondrial Fatty Acid Beta-Oxidation / phosphatidylcholine binding / phospholipid transport / negative regulation of cold-induced thermogenesis / lipid transport / Synthesis of PC / cytosol
Similarity search - Function
STARD2, START domain / : / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Phosphatidylcholine transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRoderick, S.L. / Chan, W.W. / Agate, D.S. / Olsen, L.R. / Vetting, M.W. / Rajashankar, K.R. / Cohen, D.E.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Structure of human phosphatidylcholine transfer protein in complex with its ligand.
Authors: Roderick, S.L. / Chan, W.W. / Agate, D.S. / Olsen, L.R. / Vetting, M.W. / Rajashankar, K.R. / Cohen, D.E.
History
DepositionMay 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylcholine transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6532
Polymers24,8711
Non-polymers7821
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.300, 133.300, 83.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Phosphatidylcholine transfer protein / PC-TP


Mass: 24871.301 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) / References: UniProt: Q9UKL6
#2: Chemical ChemComp-DLP / 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DI-LINOLEOYL-3-SN-PHOSPHATIDYLCHOLINE


Mass: 782.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H80NO8P / Comment: phospholipid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: sodium formate, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 5.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13.4-3.8 Msodium formate1reservoir
20.1 Msodium acetate1reservoirpH5.7
35 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 117 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.94645 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 16, 2001
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94645 Å / Relative weight: 1
ReflectionResolution: 2.4→25.4 Å / Num. all: 14602 / Num. obs: 14602 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.036
Reflection shellResolution: 2.4→2.55 Å / % possible all: 99.6
Reflection
*PLUS
Num. measured all: 135402
Reflection shell
*PLUS
Lowest resolution: 2.49 Å / % possible obs: 99.6 % / Rmerge(I) obs: 0.231

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
X-PLORmodel building
CNS1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→25.38 Å / Rfactor Rfree error: 0.011 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 695 5 %RANDOM
Rwork0.234 ---
all0.237 13848 --
obs0.237 13848 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.2738 Å2 / ksol: 0.397764 e/Å3
Refine analyzeLuzzati coordinate error free: 0.47 Å / Luzzati sigma a free: 0.52 Å
Refinement stepCycle: LAST / Resolution: 2.4→25.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1670 0 54 34 1758
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.181.5
X-RAY DIFFRACTIONc_mcangle_it4.782
X-RAY DIFFRACTIONc_scbond_it4.762
X-RAY DIFFRACTIONc_scangle_it6.162.5
LS refinement shellHighest resolution: 2.4 Å / Total num. of bins used: 6 /
Num. reflection% reflection
Rwork1991 -
Rfree-5.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PC2_NEW.PARPC2.TOP
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rwork: 0.237
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.06
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.49 Å / Rfactor Rfree: 0.406 / Rfactor Rwork: 0.384

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