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BMRB: 17430

2L8X

Spatial structure of antimicrobial peptide Arenicin-2 dimer in DPC micelles

Authors

Shenkarev, Z.O., Trunov, K.I., Paramonov, A.S., Arseniev, A.S.

Assembly

Arenicin-2 dimer

Entity

1. Arenicin-2 dimer (polymer), 21 monomers, 2774.324 × 2 Da Detail

RWCVYAYVRI RGVLVRYRRC W

Total weight

5548.648 Da

Max. entity weight

2774.324 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS3:SG	1:CYS20:SG
2	disulfide	sing	1:CYS3:SG	1:CYS20:SG

Source organism

Arenicola marina

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 91.8 %, Completeness (bb): 93.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.8 % (256 of 279)	93.2 % (136 of 146)	89.1 % (98 of 110)	95.7 % (22 of 23)
Backbone	93.7 % (118 of 126)	93.0 % (40 of 43)	93.5 % (58 of 62)	95.2 % (20 of 21)
Sidechain	90.8 % (157 of 173)	93.2 % (96 of 103)	86.8 % (59 of 68)	100.0 % (2 of 2)
Aromatic	87.5 % (42 of 48)	100.0 % (24 of 24)	72.7 % (16 of 22)	100.0 % (2 of 2)
Methyl	96.2 % (25 of 26)	100.0 % (13 of 13)	92.3 % (12 of 13)

1. Arenicin-2

RWCVYAYVRI RGVLVRYRRC W

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 316 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	Arenicin-2	[U-100% 13C; U-100% 15N]		1.2 mM
2	Dodecil phosphocholine	[U-2H]		120 mM
3	D2O	natural abundance		100 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 316 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
4	Arenicin-2	[U-100% 15N]		1.2 mM
5	Dodecil phosphocholine	[U-2H]		120 mM
6	D2O	natural abundance		5 %
7	H2O	natural abundance		95 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 316 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
8	Arenicin-2	[U-100% 13C; U-100% 15N]		1.2 mM
9	Dodecil phosphocholine	[U-2H]		120 mM
10	D2O	natural abundance		5 %
11	H2O	natural abundance		95 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2L8X, Strand ID: A, B Detail

Release date

2011-06-06

Citation

Molecular mechanism of action of β-hairpin antimicrobial peptide arenicin: oligomeric structure in dodecylphosphocholine micelles and pore formation in planar lipid bilayers
Shenkarev, Z.O., Balandin, S.V., Trunov, K.I., Paramonov, A.S., Sukhanov, S.V., Barsukov, L.I., Arseniev, A.S., Ovchinnikova, T.V.
Biochemistry (2011), 50, 6255-6265, PubMed 21627330 , DOI 10.1021/bi200746t , Abstract

Related entities 1. Arenicin-2 dimer, : 1 : 2 : 2 : 6 entities Detail

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 316 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
4	Arenicin-2	[U-100% 15N]		1.2 mM
5	Dodecil phosphocholine	[U-2H]		120 mM
6	D2O	natural abundance		5 %
7	H2O	natural abundance		95 %

2 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 316 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
8	Arenicin-2	[U-100% 13C; U-100% 15N]		1.2 mM
9	Dodecil phosphocholine	[U-2H]		120 mM
10	D2O	natural abundance		5 %
11	H2O	natural abundance		95 %

3 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 316 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
8	Arenicin-2	[U-100% 13C; U-100% 15N]		1.2 mM
9	Dodecil phosphocholine	[U-2H]		120 mM
10	D2O	natural abundance		5 %
11	H2O	natural abundance		95 %

4 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 316 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
8	Arenicin-2	[U-100% 13C; U-100% 15N]		1.2 mM
9	Dodecil phosphocholine	[U-2H]		120 mM
10	D2O	natural abundance		5 %
11	H2O	natural abundance		95 %

5 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 316 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
8	Arenicin-2	[U-100% 13C; U-100% 15N]		1.2 mM
9	Dodecil phosphocholine	[U-2H]		120 mM
10	D2O	natural abundance		5 %
11	H2O	natural abundance		95 %

6 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 316 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
4	Arenicin-2	[U-100% 15N]		1.2 mM
5	Dodecil phosphocholine	[U-2H]		120 mM
6	D2O	natural abundance		5 %
7	H2O	natural abundance		95 %

7 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 316 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
8	Arenicin-2	[U-100% 13C; U-100% 15N]		1.2 mM
9	Dodecil phosphocholine	[U-2H]		120 mM
10	D2O	natural abundance		5 %
11	H2O	natural abundance		95 %

NMR combined restraints 9 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17430_2l8x.nef
Input source #2: Coordindates	2l8x.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:20:CYS:SG	oxidized, CA 55.809, CB 49.0 ppm	oxidized, CA 55.959, CB 48.313 ppm	1.985
B:33:CYS:SG	B:50:CYS:SG	oxidized, CA 56.089, CB 50.0 ppm	oxidized, CA 56.165, CB 48.203 ppm	2.061

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-
RWCVYAYVRIRGVLVRYRRCW
|||||||||||||||||||||
RWCVYAYVRIRGVLVRYRRCW

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

--------40--------50-
RWCVYAYVRIRGVLVRYRRCW
|||||||||||||||||||||
RWCVYAYVRIRGVLVRYRRCW
--------10--------20-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	21	0	0	100.0
B	B	21	0	0	100.0

Content subtype: combined_17430_2l8x.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_chem_shift_list_1	Warning	548		100.0 (chain: A, length: 21), 100.0 (chain: B, length: 21)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	721 (1)	noe	100.0 (chain: A, length: 21), 100.0 (chain: B, length: 21)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	6 (1)	disulfide_bond	9.5 (chain: A, length: 21), 9.5 (chain: B, length: 21)
3	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	1 (1)	noe	9.5 (chain: A, length: 21)
4	Distance restraints	DYANA/DIANA_distance_constraints_7	Warning	6 (1)	disulfide_bond	9.5 (chain: A, length: 21), 9.5 (chain: B, length: 21)
5	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	50 (1)	hbond	66.7 (chain: A, length: 21), 66.7 (chain: B, length: 21)
6	Distance restraints	DYANA/DIANA_distance_constraints_6	Warning	50 (1)	hbond	66.7 (chain: A, length: 21), 66.7 (chain: B, length: 21)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_8	OK	71 (71)	.	100.0 (chain: A, length: 21), 100.0 (chain: B, length: 21)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 21, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 291
  - ¹³C chemical shifts: 201
  - ¹⁵N chemical shifts: 56
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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
  - Chain_ID: B

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: 21, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 21, Sequence coverage: 100.0%
- Total number of restraints: 714
- Weight of restraints: 1.0 (714)
- Potential type of restraints: upper-bound-parabolic (714)
- Range of distance target values: 0.0, 6.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- 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: 21, Sequence coverage: 9.5%
    - Entity_assembly_ID: B, Chain length: 21, Sequence coverage: 9.5%
  - Total number of restraints: 6
  - Weight of restraints: 1.0 (6)
  - Potential type of restraints: upper-bound-parabolic (6)
  - Range of distance target values: 2.1, 3.1 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_5
    - Status: Warning
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 9.5%
    - Total number of restraints: 1
    - Weight of restraints: 1.0 (1)
    - Potential type of restraints: upper-bound-parabolic (1)
    - Range of distance target values: 3.0, 3.0 (Å)
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - Distance restraints on contact map
    - Saveframe: DYANA/DIANA_distance_constraints_7
      - Status: Warning
      - Experiment type: disulfide_bond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 9.5%
        Entity_assembly_ID: B, Chain length: 21, Sequence coverage: 9.5%
      - Total number of restraints: 6
        Long range restraints, | i - j | >= 5 : 4
        Total disulfide bond restraints: 2
      - Weight of restraints: 1.0 (6)
        Long range restraints, | i - j | >= 5 : 1.0 (4)
        Total disulfide bond restraints: 1.0 (2)
      - Potential type of restraints: upper-bound-parabolic (6)
        Long range restraints, | i - j | >= 5 : upper-bound-parabolic (4)
        Total disulfide bond restraints: upper-bound-parabolic (2)
      - Range of distance target values: 2.0, 3.0 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
        Chain_ID: B
      - Distance restraints on contact map
      - Saveframe: DYANA/DIANA_distance_constraints_3
        Status: OK
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 66.7%
        --------10--------20- RWCVYAYVRIRGVLVRYRRCW |||||||||  | | | | | .WCVYAYVRI..V.V.Y.R.W
        Entity_assembly_ID: B, Chain length: 21, Sequence coverage: 66.7%
        --------40--------50- RWCVYAYVRIRGVLVRYRRCW |||||||| |  | | | | | RWCVYAYV.I..V.V.Y.R.W
        Total number of restraints: 50
        Total hydrogen bond restraints: 50
        O...H-x: 4
        O...h-N: 4
        Long range: 28
        O...H-x: 14
        O...h-N: 14
        Inter-chain: 14
        O...H-x: 7
        O...h-N: 7
        Weight of restraints: 1.0 (50)
        Total hydrogen bond restraints: 1.0 (50)
        O...H-x: 1.0 (4)
        O...h-N: 1.0 (4)
        Long range: 1.0 (28)
        O...H-x: 1.0 (14)
        O...h-N: 1.0 (14)
        Inter-chain: 1.0 (14)
        O...H-x: 1.0 (7)
        O...h-N: 1.0 (7)
        Potential type of restraints: upper-bound-parabolic (50)
        Total hydrogen bond restraints: upper-bound-parabolic (50)
        O...H-x: upper-bound-parabolic (4)
        O...h-N: upper-bound-parabolic (4)
        Long range: upper-bound-parabolic (28)
        O...H-x: upper-bound-parabolic (14)
        O...h-N: upper-bound-parabolic (14)
        Inter-chain: upper-bound-parabolic (14)
        O...H-x: upper-bound-parabolic (7)
        O...h-N: upper-bound-parabolic (7)
        Range of distance target values: 2.3, 3.3 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Chain_ID: B
        Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A
        Chain_ID_1: B - Chain_ID_2: B
        Chain_ID_1: A - Chain_ID_2: B
        Saveframe: DYANA/DIANA_distance_constraints_6
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 66.7%
        --------10--------20- RWCVYAYVRIRGVLVRYRRCW |||||||||  | | | | | .WCVYAYVRI..V.V.Y.R.W
        Entity_assembly_ID: B, Chain length: 21, Sequence coverage: 66.7%
        --------40--------50- RWCVYAYVRIRGVLVRYRRCW |||||||| |  | | | | | RWCVYAYV.I..V.V.Y.R.W
        Total number of restraints: 50
        Total hydrogen bond restraints: 50
        O...H-x (too close!): 4
        O...h-N (too close!): 4
        Long range: 28
        O...H-x (too close!): 14
        O...h-N (too close!): 14
        Inter-chain: 14
        O...H-x (too close!): 7
        O...h-N (too close!): 7
        Weight of restraints: 1.0 (50)
        Total hydrogen bond restraints: 1.0 (50)
        O...H-x (too close!): 1.0 (4)
        O...h-N (too close!): 1.0 (4)
        Long range: 1.0 (28)
        O...H-x (too close!): 1.0 (14)
        O...h-N (too close!): 1.0 (14)
        Inter-chain: 1.0 (14)
        O...H-x (too close!): 1.0 (7)
        O...h-N (too close!): 1.0 (7)
        Potential type of restraints: upper-bound-parabolic (50)
        Total hydrogen bond restraints: upper-bound-parabolic (50)
        O...H-x (too close!): upper-bound-parabolic (4)
        O...h-N (too close!): upper-bound-parabolic (4)
        Long range: upper-bound-parabolic (28)
        O...H-x (too close!): upper-bound-parabolic (14)
        O...h-N (too close!): upper-bound-parabolic (14)
        Inter-chain: upper-bound-parabolic (14)
        O...H-x (too close!): upper-bound-parabolic (7)
        O...h-N (too close!): upper-bound-parabolic (7)
        Range of distance target values: 1.8, 2.7 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Chain_ID: B
        Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A
        Chain_ID_1: B - Chain_ID_2: B
        Chain_ID_1: A - Chain_ID_2: B

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_8
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 21, Sequence coverage: 100.0%
- Total number of restraints: 71
- Total number of restraints per polymer type: 71
- Weight of restraints: 1.0 (71)
- Potential type of restraints: square-well-parabolic (71)
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords antimicrobial peptide, arenicin, beta-hairpin, NMR, oligomerization, pore forming peptide