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- PDB-1ln3: Structure of Human Phosphatidylcholine Transfer Protein in Comple... -

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Basic information

Entry
Database: PDB / ID: 1ln3
TitleStructure of Human Phosphatidylcholine Transfer Protein in Complex with Palmitoyl-Linoleoyl Phosphatidylcholine (Seleno-Met Protein)
ComponentsPhosphatidylcholine transfer protein
KeywordsLIPID BINDING PROTEIN / START Domain
Function / homology
Function and homology information


phosphatidylcholine transporter activity / Mitochondrial Fatty Acid Beta-Oxidation / phospholipid transport / phosphatidylcholine binding / 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
Chem-CPL / Phosphatidylcholine transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 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
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylcholine transfer protein
B: Phosphatidylcholine transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9154
Polymers50,3992
Non-polymers1,5162
Water1,24369
1
A: Phosphatidylcholine transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9582
Polymers25,2001
Non-polymers7581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphatidylcholine transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9582
Polymers25,2001
Non-polymers7581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.600, 134.600, 82.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsThe biological assembly is a monomer. Two monomers are related by approximately (1/2,1/2,1/2).

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Components

#1: Protein Phosphatidylcholine transfer protein / PC-TP


Mass: 25199.564 Da / Num. of mol.: 2
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-CPL / 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / PALMITOYL-LINOLEOYL PHOSPHATIDYLCHOLINE


Mass: 758.060 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H80NO8P / Comment: phospholipid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
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: 3.71 Å3/Da / Density % sol: 66.85 %
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: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 28, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.9→27.5 Å / Num. all: 17846 / Num. obs: 17846 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.06
Reflection shellResolution: 2.9→3.08 Å / % possible all: 88
Reflection
*PLUS
Highest resolution: 2.9 Å / Num. measured all: 60811 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 83.6 % / Rmerge(I) obs: 0.19

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Processing

Software
NameClassification
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→27.53 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 796 4.9 %RANDOM
Rwork0.223 ---
all0.226 16249 --
obs0.226 16249 93.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.0871 Å2 / ksol: 0.356755 e/Å3
Refine analyzeLuzzati coordinate error free: 0.44 Å / Luzzati sigma a free: 0.65 Å
Refinement stepCycle: LAST / Resolution: 2.9→27.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3340 0 104 69 3513
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.11.5
X-RAY DIFFRACTIONc_mcangle_it6.282
X-RAY DIFFRACTIONc_scbond_it8.062
X-RAY DIFFRACTIONc_scangle_it9.92.5
LS refinement shellHighest resolution: 2.9 Å / Total num. of bins used: 6 /
Num. reflection% reflection
Rwork2368 -
Rfree-4.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PLC_NEW.PARPLC_NEW.TOP
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rwork: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3.08 Å / Rfactor Rfree: 0.361 / Rfactor Rwork: 0.279

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