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- PDB-2ktd: Solution structure of mouse lipocalin-type prostaglandin D syntha... -

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Basic information

Entry
Database: PDB / ID: 2ktd
TitleSolution structure of mouse lipocalin-type prostaglandin D synthase / substrate analog (U-46619) complex
ComponentsProstaglandin-H2 D-isomerase
KeywordsISOMERASE / lipocalin-type prostaglandin D synthase / L-PGDS / Prostaglandin H2 / Prostaglandin D2 / U-46619 / lipocalin / Disulfide bond / Endoplasmic reticulum / Fatty acid biosynthesis / Glycoprotein / Golgi apparatus / Lipid synthesis / Nucleus / Prostaglandin biosynthesis / Pyrrolidone carboxylic acid / Secreted / Transport
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 / rough endoplasmic reticulum / response to glucocorticoid ...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 / rough endoplasmic reticulum / response to glucocorticoid / 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
Chem-PUC / Prostaglandin-H2 D-isomerase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsShimamoto, S. / Maruo, H. / Yoshida, T. / Kato, N. / Ohkubo, T.
CitationJournal: To be Published
Title: Solution Structure of Lipocalin-type Prostaglandin D synthase / Substrate analog complex reveals Open-Closed Conformational Change required for Substrate Recognition
Authors: Shimamoto, S. / Maruo, H. / Yoshida, T. / Inui, T. / Miyamoto, Y. / Kobayashi, Y. / Tsurumura, T. / Aritake, K. / Urade, Y. / Ohkubo, T.
History
DepositionJan 27, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: Prostaglandin-H2 D-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9362
Polymers18,5861
Non-polymers3501
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 1500structures 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) / Gene: Ptgds / Production host: Escherichia coli (E. coli) / References: UniProt: O09114, prostaglandin-D synthase
#2: Chemical ChemComp-PUC / (5Z)-7-{(1R,4S,5S,6R)-6-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-2-oxabicyclo[2.2.1]hept-5-yl}hept-5-enoic acid / 15-Hydroxy-11 alpha,9 alpha-(epoxymethano)prosta-5,13-dienoic Acid


Mass: 350.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H34O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HN(CA)CB
1323D CBCA(CO)NH
1423D (H)CCH-TOCSY
1513D 1H-15N NOESY
1623D 1H-13C NOESY
1723D HBHA(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM [U-15N] protein; 1.5mM 15-hydroxy-11alpha,9alpha-(epoxymethano)prosta-5,13-dienoic acid; 90% H2O/10% D2O90% H2O/10% D2O
21.0mM [U-13C; U-15N] protein; 1.5mM 15-hydroxy-11alpha,9alpha-(epoxymethano)prosta-5,13-dienoic acid; 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMentity_1-1[U-15N]1
1.5 mM15-hydroxy-11alpha,9alpha-(epoxymethano)prosta-5,13-dienoic acid-21
1.0 mMentity_1-3[U-13C; U-15N]2
1.5 mM15-hydroxy-11alpha,9alpha-(epoxymethano)prosta-5,13-dienoic acid-42
Sample conditionspH: 7.0 / Pressure: 1 atm / Temperature: 300.5 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 software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1500 / Conformers submitted total number: 15 / Representative conformer: 1

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