BMRBj - BMREntryMaster

	Total	¹H	¹³C
All	89.7 % (235 of 262)	100.0 % (151 of 151)	75.7 % (84 of 111)
Backbone	81.9 % (122 of 149)	100.0 % (67 of 67)	67.1 % (55 of 82)
Sidechain	100.0 % (135 of 135)	100.0 % (84 of 84)	100.0 % (51 of 51)
Aromatic	100.0 % (32 of 32)	100.0 % (16 of 16)	100.0 % (16 of 16)
Methyl	100.0 % (10 of 10)	100.0 % (5 of 5)	100.0 % (5 of 5)

1. SmAMP2-2c

AAGQCYRGRC SGGLCCSKYG YCGSGPAYCG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 (±1) K, pH 4.5 (±0.05)

#	Name	Isotope labeling	Concentration
1	SmAMP2-2c	natural abundance	0.8 (±0.1) mM
2	sodium acetate	natural abundance	20 (±0.1) mM
3	sodium chloride	natural abundance	30 (±0.1) mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 (±1) K, pH 4.5 (±0.05)

#	Name	Isotope labeling	Concentration
4	SmAMP2-2c	natural abundance	0.8 (±0.1) mM
5	sodium acetate	natural abundance	20 (±0.1) mM
6	sodium chloride	natural abundance	30 (±0.1) mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 (±1) K, pH 4.5 (±0.05)

#	Name	Isotope labeling	Concentration
7	SmAMP2-2c	natural abundance	2 (±0.1) mM
8	sodium acetate	natural abundance	10 (±0.1) mM
9	sodium chloride	natural abundance	70 (±0.1) mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2N1S, Strand ID: A Detail

Release date

2016-06-26

Citation

Common chickweed (Stellaria media) antifungal peptides with chitin-binding domain provide unique plant defense strategy
Vassilevski, A.A., Bozin, T.N., Musolyamov, A.K., Panova, S.V., Slavokhotova, A.A., Mitkevich, V.A., Finkina, E.I., Nikonorova, A.K., Ovchinnikova, T.V., Arseniev, A.S., Babakov, A.V., Bocharov, E.V., Grishin, E.V., Egorov, T.A.
Molecular Plant

Related entities 1. Antimicrobial Peptide SmAMP2-2c, : 1 : 20 entities Detail

Experiments performed 6 experiments Detail

NMR combined restraints 8 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25574_2n1s.nef
Input source #2: Coordindates	2n1s.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:16:CYS:SG	oxidized, CA 54.848, CB 41.396 ppm	oxidized, CA 55.835, CB 41.284 ppm	2.104
A:5:CYS:SG	A:10:CYS:SG	oxidized, CA 54.848, CB 41.396 ppm	oxidized, CA 54.466, CB 46.281 ppm	2.951
A:10:CYS:SG	A:22:CYS:SG	oxidized, CA 54.466, CB 46.281 ppm	oxidized, CA 54.074, CB 43.146 ppm	2.013
A:15:CYS:SG	A:29:CYS:SG	oxidized, CA 54.052, CB 50.309 ppm	oxidized, CA 54.982, CB 43.058 ppm	1.994

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--------30
AAGQCYRGRCSGGLCCSKYGYCGSGPAYCG
||||||||||||||||||||||||||||||
AAGQCYRGRCSGGLCCSKYGYCGSGPAYCG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	30	0	0	100.0

Content subtype: combined_25574_2n1s.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	233		100.0 (chain: A, length: 30)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	2169 (1)	noe	100.0 (chain: A, length: 30)
2	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	9 (1)	undefined	20.0 (chain: A, length: 30)
3	Distance restraints	DYANA/DIANA_distance_constraints_7	Warning	9 (1)	undefined	20.0 (chain: A, length: 30)
4	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	32 (1)	hbond	63.3 (chain: A, length: 30)
5	Distance restraints	DYANA/DIANA_distance_constraints_6	OK	32 (1)	hbond	63.3 (chain: A, length: 30)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	Warning	92 (89)	.	90.0 (chain: A, length: 30)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 152
  - ¹³C chemical shifts: 81
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
17	SER	HG	6.276

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	151	150	99.3
¹³C chemical shifts	111	81	73.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	67	66	98.5
¹³C chemical shifts	60	30	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	84	84	100.0
¹³C chemical shifts	51	51	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	5	100.0
¹³C chemical shifts	5	5	100.0

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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 100.0%
- Total number of restraints: 2147
- Weight of restraints: 1.0 (2147)
- Potential type of restraints: upper-bound-parabolic (2147)
- Range of distance target values: 2.4, 7.94 (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_5
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 20.0%
  - Total number of restraints: 9
  - Weight of restraints: 1.0 (9)
  - Potential type of restraints: upper-bound-parabolic (9)
  - 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
  - Saveframe: DYANA/DIANA_distance_constraints_7
    - Status: Warning
    - Experiment type: undefined
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 20.0%
    - Total number of restraints: 9
    - Weight of restraints: 1.0 (9)
    - Potential type of restraints: upper-bound-parabolic (9)
    - Range of distance target values: 2.1, 3.1 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map
    - Saveframe: DYANA/DIANA_distance_constraints_4
      - Status: Warning
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 63.3%
        --------10--------20--------30 AAGQCYRGRCSGGLCCSKYGYCGSGPAYCG | || | | || | |||||||| ||| ..G.CY..R.S..LC.S.YGYCGSGP.YCG
      - Total number of restraints: 32
        Total hydrogen bond restraints: 32
        O...H-x (too close!): 12
        O...h-N (too close!): 11
        O...h-O (too close!): 1
        Long range: 8
        O...H-x (too close!): 4
        O...h-N (too close!): 4
      - Weight of restraints: 1.0 (32)
        Total hydrogen bond restraints: 1.0 (32)
        O...H-x (too close!): 1.0 (12)
        O...h-N (too close!): 1.0 (11)
        O...h-O (too close!): 1.0 (1)
        Long range: 1.0 (8)
        O...H-x (too close!): 1.0 (4)
        O...h-N (too close!): 1.0 (4)
      - Potential type of restraints: upper-bound-parabolic (32)
        Total hydrogen bond restraints: upper-bound-parabolic (32)
        O...H-x (too close!): upper-bound-parabolic (12)
        O...h-N (too close!): upper-bound-parabolic (11)
        O...h-O (too close!): upper-bound-parabolic (1)
        Long range: upper-bound-parabolic (8)
        O...H-x (too close!): upper-bound-parabolic (4)
        O...h-N (too close!): upper-bound-parabolic (4)
      - Range of distance target values: 1.8, 2.7 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
      - Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A
      - Saveframe: DYANA/DIANA_distance_constraints_6
        Status: OK
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 63.3%
        --------10--------20--------30 AAGQCYRGRCSGGLCCSKYGYCGSGPAYCG | || | | || | |||||||| ||| ..G.CY..R.S..LC.S.YGYCGSGP.YCG
        Total number of restraints: 32
        Total hydrogen bond restraints: 32
        O...H-x: 12
        O...h-N: 11
        O...h-O: 1
        Long range: 8
        O...H-x: 4
        O...h-N: 4
        Weight of restraints: 1.0 (32)
        Total hydrogen bond restraints: 1.0 (32)
        O...H-x: 1.0 (12)
        O...h-N: 1.0 (11)
        O...h-O: 1.0 (1)
        Long range: 1.0 (8)
        O...H-x: 1.0 (4)
        O...h-N: 1.0 (4)
        Potential type of restraints: upper-bound-parabolic (32)
        Total hydrogen bond restraints: upper-bound-parabolic (32)
        O...H-x: upper-bound-parabolic (12)
        O...h-N: upper-bound-parabolic (11)
        O...h-O: upper-bound-parabolic (1)
        Long range: upper-bound-parabolic (8)
        O...H-x: upper-bound-parabolic (4)
        O...h-N: upper-bound-parabolic (4)
        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
        Chain_ID_1: A - Chain_ID_2: A

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 90.0%
- Total number of restraints: 89
- Total number of restraints per polymer type: 89
- Weight of restraints: 1.0 (89)
- Potential type of restraints: square-well-parabolic (89)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords AMP, Antimicrobial Peptide, ICK, Stellaria media, cystine knot, cystine knot inhibitor

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Found 1 Document (0.739 seconds)

BMRB: 25574

Sample #1

Sample #2

Sample #3

Related entities 1. Antimicrobial Peptide SmAMP2-2c, : 1 : 20 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 8 contents Detail