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Found 1 Document (1.603 seconds)

BMRB: 11062

2RQ0

Solution structure of mouse lipocalin-type prostaglandin D synthase possessing a intrinsic disulfide bond.

Authors

Miyamoto, Y., Nishimura, S., Inui, T.

Assembly

lipocalin-type prostaglandin D synthase

Entity

1. lipocalin-type prostaglandin D synthase (polymer, Thiol state: all disulfide bound), 167 monomers, 18595.65 Da Detail

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

Formula weight

18595.65 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS67:SG	1:CYS164:SG

Source organism

Mus musculus

Exptl. method

solution NMR

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.8 %, Completeness: 72.2 %, Completeness (bb): 82.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	72.2 % (1403 of 1942)	73.8 % (745 of 1009)	64.7 % (489 of 756)	95.5 % (169 of 177)
Backbone	82.8 % (816 of 986)	97.6 % (331 of 339)	67.6 % (330 of 488)	97.5 % (155 of 159)
Sidechain	66.5 % (738 of 1110)	61.8 % (414 of 670)	73.5 % (310 of 422)	77.8 % (14 of 18)
Aromatic	23.1 % (43 of 186)	28.0 % (26 of 93)	16.5 % (15 of 91)	100.0 % (2 of 2)
Methyl	84.2 % (133 of 158)	84.8 % (67 of 79)	83.5 % (66 of 79)

1. lipocalin-type prostaglandin D synthase

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

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4

#	Name	Isotope labeling	Concentration
1	Prostaglandin-H2 D-isomerase	[U-13C; U-15N]	0.5 mM
2	acetic acid	[U-2H]	20 mM
3	H2O		90 %
4	D2O		10 %

Sample #2

Solvent system 99.9% D2O, Pressure 1 atm, Temperature 298 K, pH 4

#	Name	Isotope labeling	Concentration
5	Prostaglandin-H2 D-isomerase	[U-13C; U-15N]	0.5 mM
6	acetic acid	[U-2H]	20 mM
7	D2O		99.9 %

LACS Plot; CA

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

Referencing offset: 0.1 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: 0.1 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.11 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2RQ0, Strand ID: A Detail

Release date

2010-01-10

Citation

Structural analysis of lipocalin-type prostaglandin D synthase complexed with biliverdin by small-angle X-ray scattering and multi-dimensional NMR
Miyamoto, Y., Nishimura, S., Inoue, K., Shimamoto, S., Yoshida, T., Fukuhara, A., Yamada, M., Urade, Y., Yagi, N., Ohkubo, T., Inui, T.
J. Struct. Biol. (2010), 169, 209-218, PubMed 19833210 , DOI 10.1016/j.jsb.2009.10.005 , Abstract

Entries sharing articles Swiss-Prot: 1 entries Detail

Swiss-Prot: O09114 released on 1997-11-01
Title PTGDS_MOUSE Entity Prostaglandin-H2 D-isomerase

Related entities 1. lipocalin-type prostaglandin D synthase, : 1 : 2 : 2 : 242 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4

#	Name	Isotope labeling	Concentration
1	Prostaglandin-H2 D-isomerase	[U-13C; U-15N]	0.5 mM
2	acetic acid	[U-2H]	20 mM
3	H2O		90 %
4	D2O		10 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 99.9% D2O, Pressure 1 atm, Temperature 298 K, pH 4

#	Name	Isotope labeling	Concentration
5	Prostaglandin-H2 D-isomerase	[U-13C; U-15N]	0.5 mM
6	acetic acid	[U-2H]	20 mM
7	D2O		99.9 %

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4

#	Name	Isotope labeling	Concentration
1	Prostaglandin-H2 D-isomerase	[U-13C; U-15N]	0.5 mM
2	acetic acid	[U-2H]	20 mM
3	H2O		90 %
4	D2O		10 %

4 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4

#	Name	Isotope labeling	Concentration
1	Prostaglandin-H2 D-isomerase	[U-13C; U-15N]	0.5 mM
2	acetic acid	[U-2H]	20 mM
3	H2O		90 %
4	D2O		10 %

5 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4

#	Name	Isotope labeling	Concentration
1	Prostaglandin-H2 D-isomerase	[U-13C; U-15N]	0.5 mM
2	acetic acid	[U-2H]	20 mM
3	H2O		90 %
4	D2O		10 %

6 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 99.9% D2O, Pressure 1 atm, Temperature 298 K, pH 4

#	Name	Isotope labeling	Concentration
5	Prostaglandin-H2 D-isomerase	[U-13C; U-15N]	0.5 mM
6	acetic acid	[U-2H]	20 mM
7	D2O		99.9 %

7 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4

#	Name	Isotope labeling	Concentration
1	Prostaglandin-H2 D-isomerase	[U-13C; U-15N]	0.5 mM
2	acetic acid	[U-2H]	20 mM
3	H2O		90 %
4	D2O		10 %

8 3D 1H-15N TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4

#	Name	Isotope labeling	Concentration
1	Prostaglandin-H2 D-isomerase	[U-13C; U-15N]	0.5 mM
2	acetic acid	[U-2H]	20 mM
3	H2O		90 %
4	D2O		10 %

9 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 99.9% D2O, Pressure 1 atm, Temperature 298 K, pH 4

#	Name	Isotope labeling	Concentration
5	Prostaglandin-H2 D-isomerase	[U-13C; U-15N]	0.5 mM
6	acetic acid	[U-2H]	20 mM
7	D2O		99.9 %

nullKeywords conformational change, molecular modeling, NMR, SAXS, structural flexibility

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Found 1 Document (1.603 seconds)

BMRB: 11062

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles Swiss-Prot: 1 entries Detail

Related entities 1. lipocalin-type prostaglandin D synthase, : 1 : 2 : 2 : 242 entities Detail

Experiments performed 9 experiments Detail

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