BMRB Entry 11062

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR11062
MolProbity Validation Chart

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Title:
Solution structure of mouse lipocalin-type prostaglandin D synthase possessing a intrinsic disulfide bond.
Deposition date:
2008-12-24
Original release date:
2010-01-11
Authors:
Miyamoto, Yuya; Nishimura, Shigenori; Inui, Takashi
Citation:

Citation: Miyamoto, Yuya; Nishimura, Shigenori; Inoue, Katsuaki; Shimamoto, Shigeru; Yoshida, Takuya; Fukuhara, Ayano; Yamada, Mao; Urade, Yoshihiro; Yagi, Naoto; Ohkubo, Tadayasu; Inui, Takashi. "Structural analysis of lipocalin-type prostaglandin D synthase complexed with biliverdin by small-angle X-ray scattering and multi-dimensional NMR"  J. Struct. Biol. 169, 209-218 (2010).
PubMed: 19833210

Assembly members:

Assembly members:
lipocalin-type prostaglandin D synthase, polymer, 167 residues, 18500 Da.

Natural source:

Natural source:   Common Name: Mouse   Taxonomy ID: 10090   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Mus musculus

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pGEX-2T

Entity Sequences (FASTA):

Entity Sequences (FASTA):
lipocalin-type prostaglandin D synthase: GSQGHDTVQPNFQQDKFLGR WYSAGLASNSSWFREKKAVL YMAKTVVAPSTEGGLNLTST FLRKNQCETKIMVLQPAGAP GHYTYSSPHSGSIHSVSVVE ANYDEYALLFSRGTKGPGQD FRMATLYSRTQTLKDELKEK FTTFSKAQGLTEEDIVFLPQ PDKCIQE

Data sets:
Data typeCount
13C chemical shifts465
15N chemical shifts165
1H chemical shifts841

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1lipocalin-type prostaglandin D synthase1

Entities:

Entity 1, lipocalin-type prostaglandin D synthase 167 residues - 18500 Da.

1   GLYSERGLNGLYHISASPTHRVALGLNPRO
2   ASNPHEGLNGLNASPLYSPHELEUGLYARG
3   TRPTYRSERALAGLYLEUALASERASNSER
4   SERTRPPHEARGGLULYSLYSALAVALLEU
5   TYRMETALALYSTHRVALVALALAPROSER
6   THRGLUGLYGLYLEUASNLEUTHRSERTHR
7   PHELEUARGLYSASNGLNCYSGLUTHRLYS
8   ILEMETVALLEUGLNPROALAGLYALAPRO
9   GLYHISTYRTHRTYRSERSERPROHISSER
10   GLYSERILEHISSERVALSERVALVALGLU
11   ALAASNTYRASPGLUTYRALALEULEUPHE
12   SERARGGLYTHRLYSGLYPROGLYGLNASP
13   PHEARGMETALATHRLEUTYRSERARGTHR
14   GLNTHRLEULYSASPGLULEULYSGLULYS
15   PHETHRTHRPHESERLYSALAGLNGLYLEU
16   THRGLUGLUASPILEVALPHELEUPROGLN
17   PROASPLYSCYSILEGLNGLU

Samples:

sample_1: Prostaglandin-H2 D-isomerase, [U-13C; U-15N], 0.5 mM; acetic acid, [U-2H], 20 mM; H2O 90%; D2O 10%

sample_2: Prostaglandin-H2 D-isomerase, [U-13C; U-15N], 0.5 mM; acetic acid, [U-2H], 20 mM; D2O 99.9%

sample_conditions_1: ionic strength: 0.02 M; pH: 4; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1

Software:

SPARKY v3.115, Goddard - chemical shift assignment

CNS v1.2., Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

NMR spectrometers:

  • Varian INOVA 600 MHz

Related Database Links:

BMRB 10137 18473
PDB
DBJ BAA74461 BAE20833
EMBL CAA61506 CAA71226
GB AAH38083 AAH43015 EDL08248 EDL08250 EDL08251
REF NP_032989 XP_006497849 XP_006497850
SP O09114
AlphaFold O09114

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks