[English] 日本語
Yorodumi
- PDB-2rq0: Solution Structure of Mouse Lipocalin-type Prostaglandin D Syntha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rq0
TitleSolution Structure of Mouse Lipocalin-type Prostaglandin D Synthase Possessing the Intrinsic Disulfide Bond
ComponentsProstaglandin-H2 D-isomerase
KeywordsISOMERASE / Lipocalin / beta-barrel / Cytoplasm / Endoplasmic reticulum / Fatty acid biosynthesis / Glycoprotein / Golgi apparatus / Lipid synthesis / Membrane / 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 / 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 / simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsMiyamoto, Y. / Nishimura, S. / Inui, T.
CitationJournal: J.Struct.Biol. / Year: 2009
Title: Structural analysis of lipocalin-type prostaglandin D synthase complexed with biliverdin by small-angle X-ray scattering and multi-dimensional NMR.
Authors: Miyamoto, Y. / Nishimura, S. / Inoue, K. / Shimamoto, S. / Yoshida, T. / Fukuhara, A. / Yamada, M. / Urade, Y. / Yagi, N. / Ohkubo, T. / Inui, T.
History
DepositionDec 24, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Prostaglandin-H2 D-isomerase


Theoretical massNumber of molelcules
Total (without water)18,6181
Polymers18,6181
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 3000structures with the lowest energy
RepresentativeModel #1lowest energy

-
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: 18617.859 Da / Num. of mol.: 1 / Mutation: C65A
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

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HBHA(CO)NH
1623D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-15N TOCSY
1923D 1H-13C NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-13C; U-15N] Prostaglandin-H2 D-isomerase-1, 20 mM [U-2H] acetic acid-2, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-13C; U-15N] Prostaglandin-H2 D-isomerase-3, 20 mM [U-2H] acetic acid-4, 99.9% D2O99.9% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMProstaglandin-H2 D-isomerase-1[U-13C; U-15N]1
20 mMacetic acid-2[U-2H]1
0.5 mMProstaglandin-H2 D-isomerase-3[U-13C; U-15N]2
20 mMacetic acid-4[U-2H]2
Sample conditionsIonic strength: 0.02 / pH: 4 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

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

-
Processing

NMR software
NameVersionClassification
CNS1.2refinement
CNS1.2structure solution
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 3000 / Conformers submitted total number: 10 / Representative conformer: 1

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more