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BMRB: 25630

2N2Z

NMR spatial structure of nonspecific lipid transfer protein from the dill Anethum graveolens L.

Authors

Mineev, K.S., Melnikova, D.N., Finkina, E.I., Arseniev, A.S., Ovchinnikova, T.V.

Assembly

nonspecific lipid transport protein from the dill Anethum graveolens L.

Entity

1. nonspecific lipid transport protein from the dill Anethum graveolens L. (polymer, Thiol state: all disulfide bound), 93 monomers, 9531.982 Da Detail

LTCGQVTGAL APCLGYLRTA GSVPVPLTCC NGVRGLNNAA RTTIDRRTAC NCLKQTANAI ADLNLNAAAG LPAKCGVNIP YKISPSTDCN RVV

Formula weight

9531.982 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS3:SG	1:CYS52:SG
2	disulfide	sing	1:CYS13:SG	1:CYS29:SG
3	disulfide	sing	1:CYS30:SG	1:CYS75:SG
4	disulfide	sing	1:CYS50:SG	1:CYS89:SG

Source organism

Anethum graveolens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.7 %, Completeness (bb): 96.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.7 % (955 of 977)	98.4 % (492 of 500)	96.6 % (366 of 379)	99.0 % (97 of 98)
Backbone	96.5 % (527 of 546)	97.3 % (183 of 188)	95.6 % (259 of 271)	97.7 % (85 of 87)
Sidechain	96.5 % (498 of 516)	96.8 % (302 of 312)	95.9 % (185 of 193)	100.0 % (11 of 11)
Aromatic	75.0 % (12 of 16)	100.0 % (8 of 8)	50.0 % (4 of 8)
Methyl	96.1 % (123 of 128)	95.3 % (61 of 64)	96.9 % (62 of 64)

1. entity

LTCGQVTGAL APCLGYLRTA GSVPVPLTCC NGVRGLNNAA RTTIDRRTAC NCLKQTANAI ADLNLNAAAG LPAKCGVNIP YKISPSTDCN RVV

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	0.5 mM
2	sodium phosphate	natural abundance	20 mM
3	glycerol	natural abundance	10 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	TSP	methyl carbon	0.0 ppm	internal	direct	1.0
¹H	water	protons	4.75 ppm	internal	direct	1.0
¹⁵N	na	nitrogen	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.58 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	TSP	methyl carbon	0.0 ppm	internal	direct	1.0
¹H	water	protons	4.75 ppm	internal	direct	1.0
¹⁵N	na	nitrogen	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.58 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	TSP	methyl carbon	0.0 ppm	internal	direct	1.0
¹H	water	protons	4.75 ppm	internal	direct	1.0
¹⁵N	na	nitrogen	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	TSP	methyl carbon	0.0 ppm	internal	direct	1.0
¹H	water	protons	4.75 ppm	internal	direct	1.0
¹⁵N	na	nitrogen	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.28 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2N2Z, Strand ID: A Detail

Release date

2016-03-27

Citation

A novel lipid transfer protein from the dill Anethum graveolens L.: isolation, structure, heterologous expression, and functional characteristics
Melnikova, D.N., Mineev, K.S., Finkina, E.I., Arseniev, A.S., Ovchinnikova, T.V.
J. Pept. Sci. (2016), 22, 59-66, PubMed 26680443 , DOI 10.1002/psc.2840 , Abstract

Related entities 1. nonspecific lipid transport protein from the dill Anethum graveolens L., : 1 : 1 : 220 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC