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- PDB-1ln2: Crystal Structure of Human Phosphatidylcholine Transfer Protein i... -

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Basic information

Entry
Database: PDB / ID: 1ln2
TitleCrystal Structure of Human Phosphatidylcholine Transfer Protein in Complex with Dilinoleoylphosphatidylcholine (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
1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Phosphatidylcholine transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 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 / Item: _software.classification / _software.name
Revision 1.4Oct 9, 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)51,9634
Polymers50,3992
Non-polymers1,5642
Water1,22568
1
A: Phosphatidylcholine transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9822
Polymers25,2001
Non-polymers7821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphatidylcholine transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9822
Polymers25,2001
Non-polymers7821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.700, 134.700, 82.700
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-DLP / 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DI-LINOLEOYL-3-SN-PHOSPHATIDYLCHOLINE


Mass: 782.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H80NO8P / Comment: phospholipid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 3.72 Å3/Da / Density % sol: 66.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: sodium formate, sodium acetate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
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: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 20, 2001
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→67.4 Å / Num. all: 16893 / Num. obs: 16893 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.048
Reflection shellResolution: 2.9→3.08 Å / Rmerge(I) obs: 0.048 / % possible all: 93.5
Reflection
*PLUS
Num. obs: 32130 / % possible obs: 99.7 % / Num. measured all: 164647 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
Lowest resolution: 3 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.128

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
MAR345data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.9→67.35 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
Rfree0.293 822 4.9 %RANDOM
Rwork0.231 ---
all0.234 16893 --
obs0.234 16893 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.9758 Å2 / ksol: 0.383111 e/Å3
Refine analyzeLuzzati coordinate error free: 0.43 Å / Luzzati sigma a free: 0.71 Å
Refinement stepCycle: LAST / Resolution: 2.9→67.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3340 0 108 68 3516
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_mcbond_it1.751.5
X-RAY DIFFRACTIONc_mcangle_it32
X-RAY DIFFRACTIONc_scbond_it3.32
X-RAY DIFFRACTIONc_scangle_it4.762.5
LS refinement shellHighest resolution: 2.9 Å / Total num. of bins used: 6 /
Num. reflection% reflection
Rwork2528 -
Rfree-5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PC2_NEW.PARPC2_NEW.TOP
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.234 / Rfactor Rfree: 0.293 / Rfactor Rwork: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.16
LS refinement shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3 Å / Rfactor Rfree: 0.454 / Rfactor Rwork: 0.333

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