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Found 1 Document (0.556 seconds)

BMRB: 25959

2NB2

nigellin-1.1

Authors

Bozin, T.N., Bocharov, E.V., Rogozhin, E.A.

Assembly

nigellin-1.1

Entity

1. nigellin-1.1 (polymer, Thiol state: all disulfide bound), 38 monomers, 4220.813 Da Detail

DRYQDCLSEC NSRCTYIPDY AGMRACIGLC APACLTSR

Formula weight

4220.813 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS6:SG	1:CYS34:SG
2	disulfide	sing	1:CYS10:SG	1:CYS30:SG
3	disulfide	sing	1:CYS14:SG	1:CYS26:SG

Source organism

Nigella sativa

Exptl. method

NMR

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 84.7 %, Completeness (bb): 78.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	84.7 % (311 of 367)	97.1 % (204 of 210)	68.2 % (107 of 157)
Backbone	78.2 % (147 of 188)	96.1 % (73 of 76)	66.1 % (74 of 112)
Sidechain	93.0 % (200 of 215)	97.8 % (131 of 134)	85.2 % (69 of 81)
Aromatic	50.0 % (12 of 24)	100.0 % (12 of 12)	0.0 % (0 of 12)
Methyl	100.0 % (32 of 32)	100.0 % (16 of 16)	100.0 % (16 of 16)

1. nigellin-1.1

DRYQDCLSEC NSRCTYIPDY AGMRACIGLC APACLTSR

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 3.5

#	Name	Isotope labeling	Concentration
1	nigellin-1.1	natural abundance	1 mM
2	sodium chloride	natural abundance	50 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 3.5

#	Name	Isotope labeling	Concentration
5	nigellin-1.1	natural abundance	1 mM
6	sodium chloride	natural abundance	50 mM
7	D2O	natural abundance	100 %

Protein Blocks Logo

Calculated from 25 models in PDB: 2NB2, Strand ID: A Detail

Release date

2016-01-25

Citation

A novel type of hairpin-like defense peptides from blackseed (Nigella sativa L.) contains three disulfide bridges
Rogozhin, E.A., Kozlov, S.A., Andreev, Y.A., Ryazantsev, D.YU., Grishin, E.V., Bozin, T.N., Bocharov, E.V.
J. Biol. Chem.

Related entities 1. nigellin-1.1, : 4 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_25959_2nb2.nef
Input source #2: Coordindates	2nb2.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:6:CYS:SG	A:34:CYS:SG	oxidized, CA 60.303, CB 37.02 ppm	oxidized, CB 39.519 ppm	1.99
A:10:CYS:SG	A:30:CYS:SG	oxidized, CA 59.671, CB 38.421 ppm	oxidized, CA 57.852, CB 38.468 ppm	1.943
A:14:CYS:SG	A:26:CYS:SG	oxidized, CB 37.752 ppm	oxidized, CA 60.16, CB 35.207 ppm	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--------30--------
DRYQDCLSECNSRCTYIPDYAGMRACIGLCAPACLTSR
||||||||||||||||||||||||||||||||||||||
DRYQDCLSECNSRCTYIPDYAGMRACIGLCAPACLTSR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	38	0	0	100.0

Content subtype: combined_25959_2nb2.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	313		100.0 (chain: A, length: 38)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2334 (1)	noe	100.0 (chain: A, length: 38)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	9 (1)	undefined	15.8 (chain: A, length: 38)
3	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	9 (1)	undefined	15.8 (chain: A, length: 38)
4	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	52 (1)	hbond	94.7 (chain: A, length: 38)
5	Distance restraints	DYANA/DIANA_distance_constraints_6	OK	52 (1)	hbond	94.7 (chain: A, length: 38)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_7	Warning	190 (172)	.	100.0 (chain: A, length: 38)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 38, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 209
  - ¹³C chemical shifts: 104
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	210	209	99.5
¹³C chemical shifts	157	104	66.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	76	75	98.7
¹³C chemical shifts	76	35	46.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	134	134	100.0
¹³C chemical shifts	81	69	85.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	17	100.0
¹³C chemical shifts	17	17	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	12	100.0
¹³C chemical shifts	12	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 38, Sequence coverage: 100.0%
- Total number of restraints: 2331
- Weight of restraints: 1.0 (2331)
- Potential type of restraints: upper-bound-parabolic (2331)
- Range of distance target values: 2.4, 6.5 (Å)
- Histogram of 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: 38, Sequence coverage: 15.8%
  - 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_5
    - Status: Warning
    - Experiment type: undefined
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 38, Sequence coverage: 15.8%
    - 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_4
      - Status: Warning
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 38, Sequence coverage: 94.7%
        --------10--------20--------30-------- DRYQDCLSECNSRCTYIPDYAGMRACIGLCAPACLTSR ||||||||||||||| | |||||||||||||||||||| DRYQDCLSECNSRCT.I.DYAGMRACIGLCAPACLTSR
      - Total number of restraints: 52
        Total hydrogen bond restraints: 52
        O...H-x (too close!): 26
        O...h-N (too close!): 26
      - Weight of restraints: 1.0 (52)
        Total hydrogen bond restraints: 1.0 (52)
        O...H-x (too close!): 1.0 (26)
        O...h-N (too close!): 1.0 (26)
      - Potential type of restraints: upper-bound-parabolic (52)
        Total hydrogen bond restraints: upper-bound-parabolic (52)
        O...H-x (too close!): upper-bound-parabolic (26)
        O...h-N (too close!): upper-bound-parabolic (26)
      - 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: 38, Sequence coverage: 94.7%
        --------10--------20--------30-------- DRYQDCLSECNSRCTYIPDYAGMRACIGLCAPACLTSR ||||||||||||||| | |||||||||||||||||||| DRYQDCLSECNSRCT.I.DYAGMRACIGLCAPACLTSR
        Total number of restraints: 52
        Total hydrogen bond restraints: 52
        O...H-x: 26
        O...h-N: 26
        Weight of restraints: 1.0 (52)
        Total hydrogen bond restraints: 1.0 (52)
        O...H-x: 1.0 (26)
        O...h-N: 1.0 (26)
        Potential type of restraints: upper-bound-parabolic (52)
        Total hydrogen bond restraints: upper-bound-parabolic (52)
        O...H-x: upper-bound-parabolic (26)
        O...h-N: upper-bound-parabolic (26)
        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_7
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 38, Sequence coverage: 100.0%
- Total number of restraints: 172
- Total number of restraints per polymer type: 172
- Weight of restraints: 1.0 (172)
- Potential type of restraints: square-well-parabolic (172)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords AMP, alpha-hairpinin, antibacterial activity, antifungal activity, antimicrobial peptide, blackseed, defense peptide, hairpin-like peptide, plant antimicrobial peptide

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Found 1 Document (0.556 seconds)

BMRB: 25959

Sample #1

Sample #2

Related entities 1. nigellin-1.1, : 4 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