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BMRB: 34027

5LM0

NMR spatial structure of Tk-hefu peptide

Authors

Mineev, K.S., Berkut, A.A., Novikova, E.V., Oparin, P.B., Grishin, E.V., Arseniev, A.S., Vassilevski, A.A.

Assembly

L-2

Entity

1. L-2 (polymer), 28 monomers, 3555.001 Da Detail

ADDRCYRMCQ RYHDRREKKQ CKEGCRYG

Formula weight

3555.001 Da

Source organism

Triticum kiharae

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.9 %, Completeness: 64.6 %, Completeness (bb): 50.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	64.6 % (219 of 339)	94.1 % (175 of 186)	13.0 % (16 of 123)	93.3 % (28 of 30)
Backbone	50.0 % (84 of 168)	93.1 % (54 of 58)	4.9 % (4 of 82)	92.9 % (26 of 28)
Sidechain	69.5 % (137 of 197)	94.5 % (121 of 128)	20.9 % (14 of 67)	100.0 % (2 of 2)
Aromatic	78.6 % (22 of 28)	100.0 % (14 of 14)	57.1 % (8 of 14)
Methyl	0.0 % (0 of 2)	0.0 % (0 of 1)	0.0 % (0 of 1)

1. entity 1

ADDRCYRMCQ RYHDRREKKQ CKEGCRYG

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.01) K, pH 5.7 (±0.1), Details 1 mM [U-99% 15N] Tk-hefu, 0.001 % sodium azide, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Tk-hefu	[U-99% 15N]		1 mM
2	sodium azide	natural abundance		0.001 %

Protein Blocks Logo

Calculated from 10 models in PDB: 5LM0, Strand ID: A Detail

Release date

2017-08-07

Citation

Structural similarity between defense peptide from wheat and scorpion neurotoxin permits rational functional design
Berkut, A.A., Chugunov, A.O., Mineev, K.S., Peigneur, S., Tabakmakher, V.M., Krylov, N.A., Oparin, P.B., Lihonosova, A.F., Novikova, E.V., Arseniev, A.S., Grishin, E.V., Tytgat, J., Efremov, R.G., Vassilevski, A.A.
J. Biol. Chem. (2014), 289, 14331-14340, PubMed 24671422 , DOI 10.1074/jbc.M113.530477 , Abstract

Related entities 1. L-2, : 1 : 5 entities Detail

Experiments performed 7 experiments Detail

1 NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.01) K, pH 5.7 (±0.1), Details 1 mM [U-99% 15N] Tk-hefu, 0.001 % sodium azide, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Tk-hefu	[U-99% 15N]		1 mM
2	sodium azide	natural abundance		0.001 %

2 2D 1H-1H TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.01) K, pH 5.7 (±0.1), Details 1 mM [U-99% 15N] Tk-hefu, 0.001 % sodium azide, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Tk-hefu	[U-99% 15N]		1 mM
2	sodium azide	natural abundance		0.001 %

3 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.01) K, pH 5.7 (±0.1), Details 1 mM [U-99% 15N] Tk-hefu, 0.001 % sodium azide, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Tk-hefu	[U-99% 15N]		1 mM
2	sodium azide	natural abundance		0.001 %

4 3D 1H-15N TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.01) K, pH 5.7 (±0.1), Details 1 mM [U-99% 15N] Tk-hefu, 0.001 % sodium azide, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Tk-hefu	[U-99% 15N]		1 mM
2	sodium azide	natural abundance		0.001 %

5 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.01) K, pH 5.7 (±0.1), Details 1 mM [U-99% 15N] Tk-hefu, 0.001 % sodium azide, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Tk-hefu	[U-99% 15N]		1 mM
2	sodium azide	natural abundance		0.001 %

6 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.01) K, pH 5.7 (±0.1), Details 1 mM [U-99% 15N] Tk-hefu, 0.001 % sodium azide, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Tk-hefu	[U-99% 15N]		1 mM
2	sodium azide	natural abundance		0.001 %

7 2D DQF-COSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.01) K, pH 5.7 (±0.1), Details 1 mM [U-99% 15N] Tk-hefu, 0.001 % sodium azide, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Tk-hefu	[U-99% 15N]		1 mM
2	sodium azide	natural abundance		0.001 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34027_5lm0.nef
Input source #2: Coordindates	5lm0.cif
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	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:5:CYS:SG	A:25:CYS:SG	unknown	unknown	1.989
A:9:CYS:SG	A:21:CYS:SG	unknown	unknown	1.991

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

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------
ADDRCYRMCQRYHDRREKKQCKEGCRYG
||||||||||||||||||||||||||||
ADDRCYRMCQRYHDRREKKQCKEGCRYG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	28	0	0	100.0

Content subtype: combined_34027_5lm0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	218		92.9 (chain: A, length: 28)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	215 (1)	noe	92.9 (chain: A, length: 28)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	6 (1)	undefined	14.3 (chain: A, length: 28)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	Warning	107 (106)	.	100.0 (chain: A, length: 28)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 28, Sequence coverage: 92.9%
- Total number of assignments
  - ¹H chemical shifts: 174
  - ¹⁵N chemical shifts: 34
  - ¹³C chemical shifts: 10
- Completeness of assignments
  - Entity_assemble_ID: A
- Tautomeric state of HIS
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 28, Sequence coverage: 92.9%
- Total number of restraints: 215
- Weight of restraints: 1.0 (215)
- Potential type of restraints: upper-bound-parabolic (215)
- Range of distance target values: 0.0, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 28, Sequence coverage: 14.3%
  - Total number of restraints: 6
  - Weight of restraints: 1.0 (6)
  - Potential type of restraints: upper-bound-parabolic (6)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 28, Sequence coverage: 100.0%
- Total number of restraints: 106
- Total number of restraints per polymer type: 106
- Weight of restraints: 1.0 (106)
- Potential type of restraints: square-well-parabolic (106)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ANTIMICROBIAL PROTEIN, PROTEIN, PROTEIN MUTANT PLANT DEFENSE PEPTIDE, anti microbial protein