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- PDB-2lq4: Structural Characterization of an LPA1 Second Extracellular Loop ... -

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Basic information

Entry
Database: PDB / ID: 2lq4
TitleStructural Characterization of an LPA1 Second Extracellular Loop Mimetic with a Self-Assembling Coiled-Coil Folding Constraint
ComponentsLysophosphatidic acid receptor 1
KeywordsDE NOVO PROTEIN / GPCR / G protein-coupled receptor
Function / homologySingle alpha-helices involved in coiled-coils or other helix-helix interfaces - #1390 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Function and homology information
Biological speciesartificial gene (others)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsYoung, J.K.
CitationJournal: Int J Mol Sci / Year: 2013
Title: Structural Characterization of an LPA1 Second Extracellular Loop Mimetic with a Self-Assembling Coiled-Coil Folding Constraint.
Authors: Young, J.K. / Clayton, B.T. / Kikonyogo, A. / Pham, T.C. / Parrill, A.L.
History
DepositionFeb 23, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2May 8, 2013Group: Structure summary
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
p: Lysophosphatidic acid receptor 1


Theoretical massNumber of molelcules
Total (without water)9,3411
Polymers9,3411
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)36 / 100all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Lysophosphatidic acid receptor 1


Mass: 9340.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HNCO
1413D HN(CA)CB
1513D HN(CO)CA
1613D H(CCO)NH
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] 21P4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: 21P4-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 50 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 100 / Conformers submitted total number: 36

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