BMRBj - BMREntryMaster

Found 1 Document (0.558 seconds)

BMRB: 30660

6U6G

Solution NMR structure of the nodule-specific cysteine-rich peptide NCR044 from Medicago truncatula

Authors

Buchko, G.W., Shah, D.M.

Assembly

Putative Late nodulin

Entity

1. Putative Late nodulin (polymer, Thiol state: all disulfide bound), 36 monomers, 4318.133 Da Detail

AFIQLSKPCI SDKECSIVKN YRARCRKGYC VRRRIR

Formula weight

4318.133 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS9:SG	1:CYS30:SG
2	disulfide	sing	1:CYS15:SG	1:CYS25:SG

Source organism

Medicago truncatula

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.8 %, Completeness (bb): 96.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.8 % (397 of 447)	83.0 % (200 of 241)	94.7 % (160 of 169)	100.0 % (37 of 37)
Backbone	96.7 % (207 of 214)	95.8 % (69 of 72)	96.3 % (103 of 107)	100.0 % (35 of 35)
Sidechain	84.0 % (225 of 268)	77.5 % (131 of 169)	94.8 % (92 of 97)	100.0 % (2 of 2)
Aromatic	100.0 % (26 of 26)	100.0 % (13 of 13)	100.0 % (13 of 13)
Methyl	100.0 % (32 of 32)	100.0 % (16 of 16)	100.0 % (16 of 16)

1. entity 1

AFIQLSKPCI SDKECSIVKN YRARCRKGYC VRRRIR

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.25) K, pH 5.4 (±0.1), Details 50 mM sodium chloride, 20 mM sodium acetate, 1 mM [U-99% 13C; U-99% 15N] DEF19, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	50 (±1.0) mM
2	sodium acetate	natural abundance	20 (±1.0) mM
3	DEF19	[U-99% 13C; U-99% 15N]	1 (±0.2) mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±0.25) K, pH 5.4 (±0.1), Details 50 mM sodium chloride, 20 mM sodium acetate, 1 mM [U-99% 13C; U-99% 15N] DEF19-2, 100% D2O

#	Name	Isotope labeling	Concentration
4	sodium chloride	natural abundance	50 (±1.0) mM
5	sodium acetate	natural abundance	20 (±1.0) mM
6	DEF19-2	[U-99% 13C; U-99% 15N]	1 (±0.2) 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: -0.41 ppm, Outliers: 2 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: -0.41 ppm, Outliers: 2 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: 0.9 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 19 models in PDB: 6U6G, Strand ID: A Detail

Release date

2019-09-30

Citation

Antifungal symbiotic peptide NCR044 exhibits unique structure and multifaceted mechanisms of action that confer plant protection
Velivelli, S., Czymmek, K.J., Li, H., Shaw, J.B., Buchko, G.W., Shah, D.M.
Proc. Natl. Acad. Sci. U. S. A. (2020), 117, 16043-16054, PubMed 32571919 , DOI 10.1073/pnas.2003526117 , Abstract

Related entities 1. Putative Late nodulin, : 1 : 9 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE - 750 MHz

Sample

State anisotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.25) K, pH 5.4 (±0.1), Details 50 mM sodium chloride, 20 mM sodium acetate, 1 mM [U-99% 13C; U-99% 15N] DEF19, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	50 (±1.0) mM
2	sodium acetate	natural abundance	20 (±1.0) mM
3	DEF19	[U-99% 13C; U-99% 15N]	1 (±0.2) mM

2 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	50 (±1.0) mM
2	sodium acetate	natural abundance	20 (±1.0) mM
3	DEF19	[U-99% 13C; U-99% 15N]	1 (±0.2) mM

3 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	50 (±1.0) mM
2	sodium acetate	natural abundance	20 (±1.0) mM
3	DEF19	[U-99% 13C; U-99% 15N]	1 (±0.2) mM

4 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	50 (±1.0) mM
2	sodium acetate	natural abundance	20 (±1.0) mM
3	DEF19	[U-99% 13C; U-99% 15N]	1 (±0.2) mM

5 2D 1H-13C HSQC aliphatic

Instrument

Bruker AVANCE - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	50 (±1.0) mM
2	sodium acetate	natural abundance	20 (±1.0) mM
3	DEF19	[U-99% 13C; U-99% 15N]	1 (±0.2) mM

6 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 750 MHz

Sample

State anisotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±0.25) K, pH 5.4 (±0.1), Details 50 mM sodium chloride, 20 mM sodium acetate, 1 mM [U-99% 13C; U-99% 15N] DEF19-2, 100% D2O

#	Name	Isotope labeling	Concentration
4	sodium chloride	natural abundance	50 (±1.0) mM
5	sodium acetate	natural abundance	20 (±1.0) mM
6	DEF19-2	[U-99% 13C; U-99% 15N]	1 (±0.2) mM

7 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	50 (±1.0) mM
2	sodium acetate	natural abundance	20 (±1.0) mM
3	DEF19	[U-99% 13C; U-99% 15N]	1 (±0.2) mM

8 Deuterium exchange

Instrument

Bruker AVANCE - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	50 (±1.0) mM
2	sodium acetate	natural abundance	20 (±1.0) mM
3	DEF19	[U-99% 13C; U-99% 15N]	1 (±0.2) mM

9 3D 1H-15N NOESY

Instrument

Bruker AVANCE - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	50 (±1.0) mM
2	sodium acetate	natural abundance	20 (±1.0) mM
3	DEF19	[U-99% 13C; U-99% 15N]	1 (±0.2) mM

10 3D 1H-13C NOESY aliphatic

Instrument

Bruker AVANCE - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	50 (±1.0) mM
2	sodium acetate	natural abundance	20 (±1.0) mM
3	DEF19	[U-99% 13C; U-99% 15N]	1 (±0.2) mM

11 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	50 (±1.0) mM
2	sodium acetate	natural abundance	20 (±1.0) mM
3	DEF19	[U-99% 13C; U-99% 15N]	1 (±0.2) mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30660_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	OK

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:9:CYS:SG	1:30:CYS:SG	oxidized, CA 54.0, CB 45.6 ppm	oxidized, CA 55.2, CB 39.5 ppm	n/a
1:15:CYS:SG	1:25:CYS:SG	oxidized, CA 53.5, CB 38.0 ppm	oxidized, CA 55.6, CB 40.3 ppm	n/a

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr30660_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	431		100.0 (chain: 1, length: 36)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 36, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 235
  - ¹³C chemical shifts: 160
  - ¹⁵N chemical shifts: 36
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	241	203	84.2
¹³C chemical shifts	169	160	94.7
¹⁵N chemical shifts	44	36	81.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	72	71	98.6
¹³C chemical shifts	72	68	94.4
¹⁵N chemical shifts	35	34	97.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	169	132	78.1
¹³C chemical shifts	97	92	94.8
¹⁵N chemical shifts	9	2	22.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	16	100.0
¹³C chemical shifts	16	16	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	13	13	100.0
¹³C chemical shifts	13	13	100.0

Keywords ANTIFUNGAL AGENT, ANTIFUNGAL PROTEIN, DEFENSIN-LIKE, FUNGAL DISEASE

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Found 1 Document (0.558 seconds)

BMRB: 30660

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Putative Late nodulin, : 1 : 9 entities Detail

Experiments performed 11 experiments Detail

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Chemical shift validation 3 contents Detail