BMRBj - BMREntryMaster

	Total	¹H	¹³C	¹⁵N
All	85.2 % (369 of 433)	97.4 % (221 of 227)	65.9 % (108 of 164)	95.2 % (40 of 42)
Backbone	82.5 % (198 of 240)	100.0 % (84 of 84)	63.8 % (74 of 116)	100.0 % (40 of 40)
Sidechain	90.0 % (206 of 229)	95.8 % (137 of 143)	82.1 % (69 of 84)	0.0 % (0 of 2)
Aromatic	42.9 % (12 of 28)	85.7 % (12 of 14)	0.0 % (0 of 14)
Methyl	100.0 % (26 of 26)	100.0 % (13 of 13)	100.0 % (13 of 13)

1. aurelin

AACSDRAHGH ICESFKSFCK DSGRNGVKLR ANCKKTCGLC

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.5) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	aurelin	[U-100% 15N]	1 mM
2	H20	natural abundance	95 %
3	D20	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.5) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
4	aurelin	[U-100% 15N]	1 mM
5	H20	natural abundance	95 %
6	D20	natural abundance	5 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 (±0.5) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
7	aurelin	[U-100% 15N]		1 mM
8	D20	natural abundance		100 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2LG4, Strand ID: A Detail

Release date

2012-08-29

Citation

Recombinant expression and solution structure of antimicrobial peptide aurelin from jellyfish Aurelia aurita
Shenkarev, Z.O., Panteleev, P.V., Balandin, S.V., Gizatullina, A.K., Altukhov, D.A., Finkina, E.I., Kokryakov, V.N., Arseniev, A.S., Ovchinnikova, T.V.
Biochem. Biophys. Res. Commun. (2012), 429, 63-69, PubMed 23137541 , DOI 10.1016/j.bbrc.2012.10.092 , Abstract

Related entities 1. aurelin, : 1 : 1 : 7 entities Detail

Experiments performed 7 experiments Detail

NMR combined restraints 11 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17792_2lg4.nef
Input source #2: Coordindates	2lg4.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:3:CYS:SG	A:40:CYS:SG	oxidized, CB 35.601 ppm	oxidized, CA 52.386, CB 36.583 ppm	1.958
A:12:CYS:SG	A:33:CYS:SG	oxidized, CA 55.303, CB 35.004 ppm	oxidized, CA 50.424, CB 35.893 ppm	2.078
A:19:CYS:SG	A:37:CYS:SG	oxidized, CA 57.371, CB 36.687 ppm	oxidized, CA 52.837, CB 32.133 ppm	1.955

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--------40
AACSDRAHGHICESFKSFCKDSGRNGVKLRANCKKTCGLC
||||||||||||||||||||||||||||||||||||||||
AACSDRAHGHICESFKSFCKDSGRNGVKLRANCKKTCGLC

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	40	0	0	100.0

Content subtype: combined_17792_2lg4.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	375		100.0 (chain: A, length: 40)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	45 (1)	noe	65.0 (chain: A, length: 40)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	3 (1)	disulfide_bond	5.0 (chain: A, length: 40)
3	Distance restraints	DYANA/DIANA_distance_constraints_6	OK	776 (1)	noe	100.0 (chain: A, length: 40)
4	Distance restraints	DYANA/DIANA_distance_constraints_7	OK	53 (1)	noe	50.0 (chain: A, length: 40)
5	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	44 (1)	hbond	72.5 (chain: A, length: 40)
6	Distance restraints	DYANA/DIANA_distance_constraints_8	Warning	45 (1)	hbond	77.5 (chain: A, length: 40)
7	Distance restraints	DYANA/DIANA_distance_constraints_10	Warning	72 (1)	hbond	70.0 (chain: A, length: 40)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	73 (73)	.	100.0 (chain: A, length: 40)
2	Dihedral angle restraints	DYANA/DIANA_dihedral_9	OK	67 (67)	.	100.0 (chain: A, length: 40)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 229
  - ¹³C chemical shifts: 107
  - ¹⁵N chemical shifts: 39
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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)
20	LYS	HZ1	7.474
20	LYS	HZ2	7.474
20	LYS	HZ3	7.474
28	LYS	HZ1	7.419
28	LYS	HZ2	7.419
28	LYS	HZ3	7.419
35	LYS	HZ1	7.466
35	LYS	HZ2	7.466
35	LYS	HZ3	7.466

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	227	220	96.9
¹³C chemical shifts	164	107	65.2
¹⁵N chemical shifts	45	39	86.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	84	83	98.8
¹³C chemical shifts	80	38	47.5
¹⁵N chemical shifts	40	39	97.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	143	137	95.8
¹³C chemical shifts	84	69	82.1
¹⁵N chemical shifts	5	0	0.0

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	14	12	85.7
¹³C chemical shifts	14	0	0.0

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: 40, Sequence coverage: 65.0%
- Total number of restraints: 45
- Weight of restraints: 1.0 (45)
- Potential type of restraints: lower-bound-parabolic (45)
- Range of distance target values: 3.0, 3.0 (Å)
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_4
  - Status: Warning
  - Experiment type: disulfide_bond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 5.0%
  - Total number of restraints: 3
  - Weight of restraints: 1.0 (3)
  - Potential type of restraints: upper-bound-parabolic (3)
  - 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_6
    - Status: OK
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 100.0%
    - Total number of restraints: 770
    - Weight of restraints: 1.0 (770)
    - Potential type of restraints: upper-bound-parabolic (770)
    - Range of distance target values: 2.4, 6.0 (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: OK
      - Experiment type: noe
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 50.0%
        --------10--------20--------30--------40 AACSDRAHGHICESFKSFCKDSGRNGVKLRANCKKTCGLC ||||| | | || || | | ||| ||| | ....DRAHG.I....K.FC.DS.R.G.KLR..CKK.C --------10--------20--------30-------
      - Total number of restraints: 53
        Intra-residue restraints, i = j : 23
        Sequential restraints, | i - j | = 1 : 14
        Backbone-backbone: 3
        Backbone-side chain: 9
        Side chain-side chain: 2
        Medium range restraints, 1 < | i - j | < 5 : 5
        Backbone-side chain: 3
        Side chain-side chain: 2
        Long range restraints, | i - j | >= 5 : 11
      - Weight of restraints: 1.0 (53)
        Intra-residue restraints, i = j : 1.0 (23)
        Sequential restraints, | i - j | = 1 : 1.0 (14)
        Backbone-backbone: 1.0 (3)
        Backbone-side chain: 1.0 (9)
        Side chain-side chain: 1.0 (2)
        Medium range restraints, 1 < | i - j | < 5 : 1.0 (5)
        Backbone-side chain: 1.0 (3)
        Side chain-side chain: 1.0 (2)
        Long range restraints, | i - j | >= 5 : 1.0 (11)
      - Potential type of restraints: lower-bound-parabolic (53)
        Intra-residue restraints, i = j : lower-bound-parabolic (23)
        Sequential restraints, | i - j | = 1 : lower-bound-parabolic (14)
        Backbone-backbone: lower-bound-parabolic (3)
        Backbone-side chain: lower-bound-parabolic (9)
        Side chain-side chain: lower-bound-parabolic (2)
        Medium range restraints, 1 < | i - j | < 5 : lower-bound-parabolic (5)
        Backbone-side chain: lower-bound-parabolic (3)
        Side chain-side chain: lower-bound-parabolic (2)
        Long range restraints, | i - j | >= 5 : lower-bound-parabolic (11)
      - Range of distance target values: 0.0, 4.26 (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
        Chain_ID_1: A - Chain_ID_2: A
      - Saveframe: DYANA/DIANA_distance_constraints_5
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 72.5%
        --------10--------20--------30--------40 AACSDRAHGHICESFKSFCKDSGRNGVKLRANCKKTCGLC     ||   ||||||| || | ||||||||||||||||| ....DR...HICESFK.FC.D.GRNGVKLRANCKKTCGL --------10--------20--------30---------
        Total number of restraints: 44
        Long range restraints, | i - j | >= 5 : 4
        Total hydrogen bond restraints: 38
        O...H-x (too close!): 16
        O...h-N (too close!): 16
        Long range: 6
        O...H-x (too close!): 3
        O...h-N (too close!): 3
        Total disulfide bond restraints: 2
        Weight of restraints: 1.0 (44)
        Long range restraints, | i - j | >= 5 : 1.0 (4)
        Total hydrogen bond restraints: 1.0 (38)
        O...H-x (too close!): 1.0 (16)
        O...h-N (too close!): 1.0 (16)
        Long range: 1.0 (6)
        O...H-x (too close!): 1.0 (3)
        O...h-N (too close!): 1.0 (3)
        Total disulfide bond restraints: 1.0 (2)
        Potential type of restraints: upper-bound-parabolic (44)
        Long range restraints, | i - j | >= 5 : upper-bound-parabolic (4)
        Total hydrogen bond restraints: upper-bound-parabolic (38)
        O...H-x (too close!): upper-bound-parabolic (16)
        O...h-N (too close!): upper-bound-parabolic (16)
        Long range: upper-bound-parabolic (6)
        O...H-x (too close!): upper-bound-parabolic (3)
        O...h-N (too close!): upper-bound-parabolic (3)
        Total disulfide bond restraints: upper-bound-parabolic (2)
        Range of distance target values: 1.8, 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
        Saveframe: DYANA/DIANA_distance_constraints_8
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 77.5%
        --------10--------20--------30--------40 AACSDRAHGHICESFKSFCKDSGRNGVKLRANCKKTCGLC   | ||   ||||||| || | |||||||||||||||||| ..C.DR...HICESFK.FC.D.GRNGVKLRANCKKTCGLC
        Total number of restraints: 45
        Long range restraints, | i - j | >= 5 : 6
        Total hydrogen bond restraints: 36
        O...H-x: 16
        O...h-N: 16
        Long range: 4
        O...H-x: 2
        O...h-N: 2
        Total disulfide bond restraints: 3
        Weight of restraints: 1.0 (45)
        Long range restraints, | i - j | >= 5 : 1.0 (6)
        Total hydrogen bond restraints: 1.0 (36)
        O...H-x: 1.0 (16)
        O...h-N: 1.0 (16)
        Long range: 1.0 (4)
        O...H-x: 1.0 (2)
        O...h-N: 1.0 (2)
        Total disulfide bond restraints: 1.0 (3)
        Potential type of restraints: upper-bound-parabolic (45)
        Long range restraints, | i - j | >= 5 : upper-bound-parabolic (6)
        Total hydrogen bond restraints: upper-bound-parabolic (36)
        O...H-x: upper-bound-parabolic (16)
        O...h-N: upper-bound-parabolic (16)
        Long range: upper-bound-parabolic (4)
        O...H-x: upper-bound-parabolic (2)
        O...h-N: upper-bound-parabolic (2)
        Total disulfide bond restraints: upper-bound-parabolic (3)
        Range of distance target values: 2.1, 3.3 (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_10
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 70.0%
        --------10--------20--------30--------40 AACSDRAHGHICESFKSFCKDSGRNGVKLRANCKKTCGLC     ||   || |||| || | ||||||||||||||||| ....DR...HI.ESFK.FC.D.GRNGVKLRANCKKTCGL --------10--------20--------30---------
        Total number of restraints: 72
        Total hydrogen bond restraints: 72
        O...H-x: 16
        O...h-N: 16
        O...H-x (too far!): 16
        O...h-N (too far!): 16
        Long range: 8
        O...H-x: 2
        O...h-N: 2
        O...H-x (too far!): 2
        O...h-N (too far!): 2
        Weight of restraints: 1.0 (72)
        Total hydrogen bond restraints: 1.0 (72)
        O...H-x: 1.0 (16)
        O...h-N: 1.0 (16)
        O...H-x (too far!): 1.0 (16)
        O...h-N (too far!): 1.0 (16)
        Long range: 1.0 (8)
        O...H-x: 1.0 (2)
        O...h-N: 1.0 (2)
        O...H-x (too far!): 1.0 (2)
        O...h-N (too far!): 1.0 (2)
        Potential type of restraints: lower-bound-parabolic (72)
        Total hydrogen bond restraints: lower-bound-parabolic (72)
        O...H-x: lower-bound-parabolic (16)
        O...h-N: lower-bound-parabolic (16)
        O...H-x (too far!): lower-bound-parabolic (16)
        O...h-N (too far!): lower-bound-parabolic (16)
        Long range: lower-bound-parabolic (8)
        O...H-x: lower-bound-parabolic (2)
        O...h-N: lower-bound-parabolic (2)
        O...H-x (too far!): lower-bound-parabolic (2)
        O...h-N (too far!): lower-bound-parabolic (2)
        Range of distance target values: 1.8, 3.3 (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
        Chain_ID_1: A - Chain_ID_2: A

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 100.0%
- Total number of restraints: 73
- Total number of restraints per polymer type: 73
- Weight of restraints: 1.0 (73)
- Potential type of restraints: square-well-parabolic (73)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: DYANA/DIANA_dihedral_9
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 100.0%
  - Total number of restraints: 67
  - Total number of restraints per polymer type: 67
  - Weight of restraints: 1.0 (67)
  - Potential type of restraints: square-well-parabolic (67)
  - Plot of Phi-Psi angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: A

Keywords antimicrobial, Protein

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BMRB: 17792

Sample #1

Sample #2

Sample #3

Related entities 1. aurelin, : 1 : 1 : 7 entities Detail

Experiments performed 7 experiments Detail

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NMR combined restraints 11 contents Detail