BMRBj - BMREntryMaster

Found 1 Document (0.543 seconds)

BMRB: 34059

5M9U

Spatial structure of antimicrobial peptide arenicin-1 mutant V8R

Authors

Myshkin, M.Y., Shenkarev, Z.O., Panteleev, P.V., Ovchinnikova, T.V.

Assembly

Arenicin-1

Entity

1. Arenicin-1 (polymer), 21 monomers, 2817.352 Da Detail

RWCVYAYRRV RGVLVRYRRC W

Formula weight

2817.352 Da

Source organism

Arenicola marina

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 89.3 %, Completeness (bb): 81.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.3 % (250 of 280)	99.3 % (147 of 148)	74.3 % (81 of 109)	95.7 % (22 of 23)
Backbone	81.0 % (102 of 126)	97.7 % (42 of 43)	64.5 % (40 of 62)	95.2 % (20 of 21)
Sidechain	96.6 % (168 of 174)	100.0 % (105 of 105)	91.0 % (61 of 67)	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	100.0 % (22 of 22)	100.0 % (11 of 11)	100.0 % (11 of 11)

1. entity 1

RWCVYAYRRV RGVLVRYRRC W

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5, Details 1.8 mM [U-99% 15N] arenicin-1 V8R, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	arenicin-1 V8R	[U-99% 15N]		1.8 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 5M9U, Strand ID: A Detail

Release date

2017-07-16

Citation

Dimerization of the antimicrobial peptide arenicin plays a key role in the cytotoxicity but not in the antibacterial activity
Panteleev, P.V., Myshkin, M.Y., Shenkarev, Z.O., Ovchinnikova, T.V.
Biochem. Biophys. Res. Commun. (2017), 482, 1320-1326, PubMed 27940358 , DOI 10.1016/j.bbrc.2016.12.035 , Abstract

Related entities 1. Arenicin-1, : 1 : 2 : 8 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceI - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5, Details 1.8 mM [U-99% 15N] arenicin-1 V8R, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	arenicin-1 V8R	[U-99% 15N]		1.8 mM

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceI - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5, Details 1.8 mM [U-99% 15N] arenicin-1 V8R, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	arenicin-1 V8R	[U-99% 15N]		1.8 mM

3 2D 1H-13C HSQC aromatic

Instrument

Bruker AvanceI - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5, Details 1.8 mM [U-99% 15N] arenicin-1 V8R, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	arenicin-1 V8R	[U-99% 15N]		1.8 mM

4 2D 1H-1H TOCSY

Instrument

Bruker AvanceI - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5, Details 1.8 mM [U-99% 15N] arenicin-1 V8R, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	arenicin-1 V8R	[U-99% 15N]		1.8 mM

5 2D 1H-1H NOESY

Instrument

Bruker AvanceI - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5, Details 1.8 mM [U-99% 15N] arenicin-1 V8R, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	arenicin-1 V8R	[U-99% 15N]		1.8 mM

6 3D 1H-15N NOESY

Instrument

Bruker AvanceI - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5, Details 1.8 mM [U-99% 15N] arenicin-1 V8R, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	arenicin-1 V8R	[U-99% 15N]		1.8 mM

7 3D HNHA

Instrument

Bruker AvanceI - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5, Details 1.8 mM [U-99% 15N] arenicin-1 V8R, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	arenicin-1 V8R	[U-99% 15N]		1.8 mM

8 3D HNHB

Instrument

Bruker AvanceI - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5, Details 1.8 mM [U-99% 15N] arenicin-1 V8R, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	arenicin-1 V8R	[U-99% 15N]		1.8 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34059_5m9u.nef
Input source #2: Coordindates	5m9u.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 52.329, CB 46.125 ppm	oxidized, CA 52.365, CB 45.441 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-
RWCVYAYRRVRGVLVRYRRCW
|||||||||||||||||||||
RWCVYAYRRVRGVLVRYRRCW

Chain assignments

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

Content subtype: combined_34059_5m9u.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	254		100.0 (chain: A, length: 21)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	276 (1)	noe	100.0 (chain: A, length: 21)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	3 (1)	undefined	9.5 (chain: A, length: 21)
3	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	39 (1)	hbond	57.1 (chain: A, length: 21)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_5	OK	396 (396)	.	100.0 (chain: A, length: 21)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 146
  - ¹³C chemical shifts: 79
  - ¹⁵N chemical shifts: 29
- 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

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%
- Total number of restraints: 276
- Weight of restraints: 1.0 (276)
- Potential type of restraints: upper-bound-parabolic (276)
- Range of distance target values: 0.0, 5.96 (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: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 9.5%
  - 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_3
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 57.1%
    - Total number of restraints: 39
    - Weight of restraints: 1.0 (39)
    - Potential type of restraints: upper-bound-parabolic (39)
    - 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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 100.0%
- Total number of restraints: 396
- Total number of restraints per polymer type: 396
- Weight of restraints: 1.0 (396)
- Potential type of restraints: square-well-parabolic (396)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords STRUCTURE FROM CYANA 3.97, antimicrobial protein