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BMRB: 30561

6NOM

NMR solution structure of Pisum sativum defensin 2 (Psd2) provides evidence for the presence of hydrophobic surface clusters

Authors

Pinheiro-Aguiar, R., Amaral, V.S.G., Bastos, I., Kurtenbach, E., Almeida, F.C.L.

Assembly

Defensin-2

Entity

1. Defensin-2 (polymer, Thiol state: all disulfide bound), 47 monomers, 5404.077 Da Detail

KTCENLSGTF KGPCIPDGNC NKHCRNNEHL LSGRCRDDFR CWCTNRC

Formula weight

5404.077 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS3:SG	1:CYS47:SG
2	disulfide	sing	1:CYS14:SG	1:CYS35:SG
3	disulfide	sing	1:CYS20:SG	1:CYS41:SG
4	disulfide	sing	1:CYS24:SG	1:CYS43:SG

Source organism

Pisum sativum

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 87.5 %, Completeness (bb): 89.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.5 % (463 of 529)	88.3 % (248 of 281)	87.2 % (171 of 196)	84.6 % (44 of 52)
Backbone	89.9 % (250 of 278)	90.6 % (87 of 96)	92.0 % (126 of 137)	82.2 % (37 of 45)
Sidechain	87.1 % (256 of 294)	87.0 % (161 of 185)	86.3 % (88 of 102)	100.0 % (7 of 7)
Aromatic	50.0 % (20 of 40)	50.0 % (10 of 20)	47.4 % (9 of 19)	100.0 % (1 of 1)
Methyl	100.0 % (22 of 22)	100.0 % (11 of 11)	100.0 % (11 of 11)

1. entity 1

KTCENLSGTF KGPCIPDGNC NKHCRNNEHL LSGRCRDDFR CWCTNRC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0, Details 1 mM [U-13C; U-15N] Psd2, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Psd2	[U-13C; U-15N]	1 (±0.005) mM
2	phosphate buffer	natural abundance	20 mM
3	NaCl	natural abundance	10 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0, Details 1 mM Psd2, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	Psd2	natural abundance	1 (±0.005) mM
5	phosphate buffer	natural abundance	20 mM
6	NaCl	natural abundance	10 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	water	protons	0.0 ppm	na	indirect	1.0

Referencing offset: 0.53 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	water	protons	0.0 ppm	na	indirect	1.0

Referencing offset: 0.53 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	water	protons	0.0 ppm	na	indirect	1.0

Referencing offset: -0.07 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	water	protons	0.0 ppm	na	indirect	1.0

Referencing offset: 0.35 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6NOM, Strand ID: A Detail

Release date

2019-08-14

Citation

Nuclear magnetic resonance solution structure of Pisum sativum defensin 2 provides evidence for the presence of hydrophobic surface-clusters
Pinheiro-Aguiar, R., do Amaral, V.S.G., Pereira, I.B., Kurtenbach, E., Almeida, F.C.L.
Proteins (2019), 88, 242-246, PubMed 31294889 , DOI 10.1002/prot.25783 , Abstract

Related entities 1. Defensin-2, : 1 : 1 : 109 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC