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- PDB-2e4j: Solution Structure of mouse Lipocalin-type Prostaglandin D Synthase -

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Basic information

Entry
Database: PDB / ID: 2e4j
TitleSolution Structure of mouse Lipocalin-type Prostaglandin D Synthase
ComponentsProstaglandin-H2 D-isomerase
KeywordsISOMERASE / PGDS
Function / homology
Function and homology information


prostaglandin-D synthase / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / regulation of circadian sleep/wake cycle, sleep / retinoid binding / prostaglandin biosynthetic process / mast cell degranulation / response to glucocorticoid / rough endoplasmic reticulum ...prostaglandin-D synthase / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / regulation of circadian sleep/wake cycle, sleep / retinoid binding / prostaglandin biosynthetic process / mast cell degranulation / response to glucocorticoid / rough endoplasmic reticulum / fatty acid binding / gene expression / nuclear membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular space / extracellular region / nucleoplasm
Similarity search - Function
Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Prostaglandin-H2 D-isomerase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, TORSION ANGLE DYNAMICS
AuthorsShimamoto, S. / Ohkubo, T.
CitationJournal: to be published
Title: Solution Structure of mouse Lipocalin-type Prostaglandin D Synthase
Authors: Shimamoto, S. / Ohkubo, T.
History
DepositionDec 11, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prostaglandin-H2 D-isomerase


Theoretical massNumber of molelcules
Total (without water)18,5861
Polymers18,5861
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 30structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Prostaglandin-H2 D-isomerase / Lipocalin-type prostaglandin-D synthase / Glutathione-independent PGD synthetase / Prostaglandin-D2 ...Lipocalin-type prostaglandin-D synthase / Glutathione-independent PGD synthetase / Prostaglandin-D2 synthase / PGD2 synthase / PGDS2 / PGDS


Mass: 18585.795 Da / Num. of mol.: 1 / Mutation: C89A, C186A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: O09114, prostaglandin-D synthase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
1223D 13C-SEPARATED NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY.

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Sample preparation

Details
Solution-IDContentsSolvent system
11MM PROTEIN U-15N, 13C; 50MM PHOSPHATE BUFFER; 85% H2O, 15% D2O85% H2O, 15% D2O
21MM PROTEIN U-15N, 13C; 50MM PHOSPHATE BUFFER WITH 5MM 2-MERCAPTOETHANOL; 99.9% D2O99.9% D2O
Sample conditionsIonic strength: 300mM NACL / pH: 6.5 / Pressure: AMBIENT / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR softwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING, TORSION ANGLE DYNAMICS
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 15

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