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BMRB: 34113

5NCE

Structure of PsDef1 defensin from Pinus sylvestris

Authors

Khairutdinov, B.I., Ermakova, E.A., Bessolitsyna, E.K., Toporkova, Y.Y., Tarasova, N.B., Kovaleva, V., Zuev, Y.F., Nesmelova, I.V.

Assembly

Defensin-1

Entity

1. Defensin-1 (polymer, Thiol state: all disulfide bound), 50 monomers, 5601.492 Da Detail

RMCKTPSGKF KGYCVNNTNC KNVCRTEGFP TGSCDFHVAG RKCYCYKPCP

Formula weight

5601.492 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS14:SG	1:CYS34:SG
2	disulfide	sing	1:CYS20:SG	1:CYS43:SG
3	disulfide	sing	1:CYS24:SG	1:CYS45:SG
4	disulfide	sing	1:CYS3:SG	1:CYS49:SG

Source organism

Pinus sylvestris

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 95.6 %, Completeness (bb): 96.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.6 % (546 of 571)	99.3 % (300 of 302)	90.0 % (197 of 219)	98.0 % (49 of 50)
Backbone	96.2 % (281 of 292)	99.0 % (100 of 101)	93.8 % (136 of 145)	97.8 % (45 of 46)
Sidechain	95.7 % (310 of 324)	99.5 % (200 of 201)	89.1 % (106 of 119)	100.0 % (4 of 4)
Aromatic	79.3 % (46 of 58)	100.0 % (29 of 29)	58.6 % (17 of 29)
Methyl	100.0 % (22 of 22)	100.0 % (11 of 11)	100.0 % (11 of 11)

1. entity 1

RMCKTPSGKF KGYCVNNTNC KNVCRTEGFP TGSCDFHVAG RKCYCYKPCP

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 306 K, pH 4.5 (±0.1), Details 0.4 mM PsDef1, 10 mM sodium acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PsDef1	natural abundance		0.4 mM
2	sodium acetate	natural abundance		10 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 306 K, pH 4.5 (±0.1), Details 0.7 mM [U-15N] PsDef1, 10 mM sodium acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	PsDef1	[U-15N]		0.7 mM
4	sodium acetate	natural abundance		10 mM

LACS Plot; CA

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

Referencing offset: -0.34 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.34 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.01 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.28 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 15 models in PDB: 5NCE, Strand ID: A Detail

Release date

2017-05-23

Citation

NMR structure, conformational dynamics, and biological activity of PsDef1 defensin from Pinus sylvestris
Khairutdinov, B.I., Ermakova, E.A., Yusypovych, Y.M., Bessolicina, E.K., Tarasova, N.B., Toporkova, Y.Y., Kovaleva, V., Zuev, Y.F., Nesmelova, I.V.
Biochim. Biophys. Acta (2017), 1865, 1085-1094, PubMed 28528214 , DOI 10.1016/j.bbapap.2017.05.012 , Abstract

Related entities 1. Defensin-1, : 1 : 1 : 145 entities Detail

Experiments performed 9 experiments Detail

1 2D DQF-COSY