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BMRB: 25468

2MZ0

Solution NMR Structure of PDFL2.1 from Arabidopsis thaliana

Authors

Omidvar, R., Bohlmann, H., Xia, Y., Veglia, G.

Assembly

PDFL2.1

Entity

1. PDFL2.1 (polymer, Thiol state: all disulfide bound), 55 monomers, 6144.166 Da Detail

KDIDGRKPLL IGTCIEFPTE KCNKTCIESN FAGGKCVHIG QSLDFVCVCF PKYYI

Formula weight

6144.166 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS14:SG	1:CYS36:SG
2	disulfide	sing	1:CYS22:SG	1:CYS47:SG
3	disulfide	sing	1:CYS26:SG	1:CYS49:SG

Source organism

Arabidopsis thaliana

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 84.1 %, Completeness (bb): 80.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.1 % (546 of 649)	97.6 % (330 of 338)	63.3 % (162 of 256)	98.2 % (54 of 55)
Backbone	80.9 % (262 of 324)	99.1 % (111 of 112)	62.5 % (100 of 160)	98.1 % (51 of 52)
Sidechain	89.1 % (334 of 375)	96.9 % (219 of 226)	76.7 % (112 of 146)	100.0 % (3 of 3)
Aromatic	41.7 % (25 of 60)	83.3 % (25 of 30)	0.0 % (0 of 30)
Methyl	100.0 % (56 of 56)	100.0 % (28 of 28)	100.0 % (28 of 28)

1. entity

KDIDGRKPLL IGTCIEFPTE KCNKTCIESN FAGGKCVHIG QSLDFVCVCF PKYYI

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM peptide in a buffer of 40 mM KCl, 20 mM KH2PO4, 1 mM NaN3 at pH 6.5.

#	Name	Isotope labeling	Concentration
1	entity	[U-13C; U-15N]	1 mM
2	potassium chloride	natural abundance	40 mM
3	potassium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	1 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

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: 2 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: 2 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: 0.0 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MZ0, Strand ID: A Detail

Release date

2016-02-14

Citation

NMR structure and conformational dynamics of AtPDFL2.1, a defensin-like peptide from Arabidopsis thaliana
Omidvar, R., Xia, Y., Porcelli, F., Bohlmann, H., Veglia, G.
Biochim. Biophys. Acta (2016), 1864, 1739-1747, PubMed 27592418 , DOI 10.1016/j.bbapap.2016.08.017 , Abstract

Related entities 1. PDFL2.1, : 1 : 2 : 6 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC