BMRB: 10137

Lipocalin-type Prostaglandin D synthase

Authors

Shimamoto, S.

Assembly

Lipocalin-type Prostaglandin D synthase

Entity

1. Lipocalin-type Prostaglandin D synthase (polymer, Thiol state: all free), 167 monomers, 18627.72 Da Detail

GSQGHDTVQP NFQQDKFLGR WYSAGLASNS SWFREKKAVL YMCKTVVAPS TEGGLNLTST FLRKNQCETK IMVLQPAGAP GHYTYSSPHS GSIHSVSVVE ANYDEYALLF SRGTKGPGQD FRMATLYSRT QTLKDELKEK FTTFSKAQGL TEEDIVFLPQ PDKCIQE

Formula weight

18627.72 Da

Source organism

Mus musculus

Exptl. method

solution NMR

Refine. method

DISTANCE GEOMETRY, SIMULATED ANNEALING, TORSION ANGLE DYNAMICS

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 75.4 %, Completeness: 57.4 %, Completeness (bb): 62.5 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	57.4 % (1115 of 1943)	59.9 % (605 of 1010)	52.6 % (398 of 756)	63.3 % (112 of 177)
Backbone	62.5 % (616 of 986)	71.4 % (242 of 339)	53.9 % (263 of 488)	69.8 % (111 of 159)
Sidechain	55.2 % (613 of 1111)	54.1 % (363 of 671)	59.0 % (249 of 422)	5.6 % (1 of 18)
Aromatic	11.8 % (22 of 186)	21.5 % (20 of 93)	2.2 % (2 of 91)	0.0 % (0 of 2)
Methyl	81.4 % (127 of 156)	83.3 % (65 of 78)	79.5 % (62 of 78)

1. L-PGDS

GSQGHDTVQP NFQQDKFLGR WYSAGLASNS SWFREKKAVL YMCKTVVAPS TEGGLNLTST FLRKNQCETK IMVLQPAGAP GHYTYSSPHS GSIHSVSVVE ANYDEYALLF SRGTKGPGQD FRMATLYSRT QTLKDELKEK FTTFSKAQGL TEEDIVFLPQ PDKCIQE

Show sample condition

Sample

Temperature 303 K, pH 6.5 (±0.3)

#	Name	Isotope labeling	Type	Concentration
1	Lipocalin-type Prostaglandin D synthase	[U-13C; U-15N]	protein	1.0 (±0.15) mM

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LACS Plot; CA

Referencing offset: 0.0 ppm, Outliers: 2 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; CB

Referencing offset: 0.0 ppm, Outliers: 2 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; HA

Referencing offset: -0.09 ppm, Outliers: 3 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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Protein Blocks Logo

Calculated from 15 models in PDB: 2E4J, Strand ID: A Detail

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Release date

2008-02-19

Citation

NMR solution structure of lipocalin-type prostaglandin D synthase: evidence for partial overlapping of catalytic pocket and retinoic acid-binding pocket within the central cavity
Shimamoto, S., Yoshida, T., Inui, T., Gohda, K., Kobayashi, Y., Fujimori, K., Tsurumura, T., Aritake, K., Urade, Y., Ohkubo, T.
J. Biol. Chem. (2007), 282, 31373-31379, PubMed 17715133 , DOI 10.1074/jbc.M700123200 , Abstract

Related entities 1. Lipocalin-type Prostaglandin D synthase, : 1 : 4 : 242 entities Detail

Experiments performed 9 experiments Detail