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BMRB: 19833

2MLV

LsbB TFE

Authors

Kristiansen, P., Ovchinnikov, K., Diep, D.

Assembly

antimicrobial peptide LsbB

Entity

1. antimicrobial peptide LsbB (polymer, Thiol state: not present), 30 monomers, 3409.956 Da Detail

MKTILRFVAG YDIASHKKKT GGYPWERGKA

Formula weight

3409.956 Da

Source organism

Lactococcus lactis

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 85.8 %, Completeness (bb): 78.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.8 % (313 of 365)	99.5 % (191 of 192)	65.0 % (93 of 143)	96.7 % (29 of 30)
Backbone	78.1 % (139 of 178)	98.4 % (62 of 63)	57.0 % (49 of 86)	96.6 % (28 of 29)
Sidechain	92.0 % (196 of 213)	100.0 % (129 of 129)	79.5 % (66 of 83)	100.0 % (1 of 1)
Aromatic	100.0 % (42 of 42)	100.0 % (21 of 21)	100.0 % (20 of 20)	100.0 % (1 of 1)
Methyl	100.0 % (26 of 26)	100.0 % (13 of 13)	100.0 % (13 of 13)

1. Molecule 1

MKTILRFVAG YDIASHKKKT GGYPWERGKA

Show sample condition

Sample

Solvent system trifluoroethanol/water, Pressure 1 atm, Temperature 298 (±0.1) K, Details LsbB in 50% TFE

#	Name	Isotope labeling	Type	Concentration
1	Molecule_1	natural abundance		1.0 (±0.1) mM
2	DSS	natural abundance		0.2 (±0.02) mM
3	H2O	natural abundance		50 %
4	TFE	[U-99% 2H]		50 %

Protein Blocks Logo

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

Release date

2014-07-13

Citation

Defining the structure and receptor binding domain of the leaderless bacteriocin LsbB
Ovchinnikov, K.V., Kristiansen, P.E., Uzelac, G., Topisirovic, L., Kojic, M., Nissen-Meyer, J., Nes, I.F., Diep, D.B.
J. Biol. Chem. (2014), 289, 23838-23845, PubMed 24993828 , DOI 10.1074/jbc.M114.579698 , Abstract

Related entities 1. antimicrobial peptide LsbB, : 1 : 1 : 5 entities Detail

Experiments performed 6 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system trifluoroethanol/water, Pressure 1 atm, Temperature 298 (±0.1) K, Details LsbB in 50% TFE

#	Name	Isotope labeling	Type	Concentration
1	Molecule_1	natural abundance		1.0 (±0.1) mM
2	DSS	natural abundance		0.2 (±0.02) mM
3	H2O	natural abundance		50 %
4	TFE	[U-99% 2H]		50 %

2 2D DQF-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system trifluoroethanol/water, Pressure 1 atm, Temperature 298 (±0.1) K, Details LsbB in 50% TFE

#	Name	Isotope labeling	Type	Concentration
1	Molecule_1	natural abundance		1.0 (±0.1) mM
2	DSS	natural abundance		0.2 (±0.02) mM
3	H2O	natural abundance		50 %
4	TFE	[U-99% 2H]		50 %

3 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system trifluoroethanol/water, Pressure 1 atm, Temperature 298 (±0.1) K, Details LsbB in 50% TFE

#	Name	Isotope labeling	Type	Concentration
1	Molecule_1	natural abundance		1.0 (±0.1) mM
2	DSS	natural abundance		0.2 (±0.02) mM
3	H2O	natural abundance		50 %
4	TFE	[U-99% 2H]		50 %

4 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system trifluoroethanol/water, Pressure 1 atm, Temperature 298 (±0.1) K, Details LsbB in 50% TFE

#	Name	Isotope labeling	Type	Concentration
1	Molecule_1	natural abundance		1.0 (±0.1) mM
2	DSS	natural abundance		0.2 (±0.02) mM
3	H2O	natural abundance		50 %
4	TFE	[U-99% 2H]		50 %

5 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system trifluoroethanol/water, Pressure 1 atm, Temperature 298 (±0.1) K, Details LsbB in 50% TFE

#	Name	Isotope labeling	Type	Concentration
1	Molecule_1	natural abundance		1.0 (±0.1) mM
2	DSS	natural abundance		0.2 (±0.02) mM
3	H2O	natural abundance		50 %
4	TFE	[U-99% 2H]		50 %

6 2D 1H-13C HMBC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system trifluoroethanol/water, Pressure 1 atm, Temperature 298 (±0.1) K, Details LsbB in 50% TFE

#	Name	Isotope labeling	Type	Concentration
1	Molecule_1	natural abundance		1.0 (±0.1) mM
2	DSS	natural abundance		0.2 (±0.02) mM
3	H2O	natural abundance		50 %
4	TFE	[U-99% 2H]		50 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19833_2mlv.nef
Input source #2: Coordindates	2mlv.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

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
MKTILRFVAGYDIASHKKKTGGYPWERGKA
||||||||||||||||||||||||||||||
MKTILRFVAGYDIASHKKKTGGYPWERGKA

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_19833_2mlv.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list	Warning	329		100.0 (chain: A, length: 30)
1	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	536 (1)	noe	100.0 (chain: A, length: 30)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	36 (36)	.	80.0 (chain: A, length: 30)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 100.0%

--------10--------20--------30
MKTILRFVAGYDIASHKKKTGGYPWERGKA
||||||||||||||||||||||||||||||
MKTILRFVAGYDIASHKKKTGGYPWERGKA

Total number of assignments
- ¹H chemical shifts: 206
- ¹³C chemical shifts: 92
- ¹⁵N chemical shifts: 31

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	LYS	HZ1	7.785
2	LYS	HZ2	7.785
2	LYS	HZ3	7.785
17	LYS	HZ1	7.629
17	LYS	HZ2	7.629
17	LYS	HZ3	7.629
18	LYS	HZ1	7.62
18	LYS	HZ2	7.62
18	LYS	HZ3	7.62
19	LYS	HZ1	7.618
19	LYS	HZ2	7.618
19	LYS	HZ3	7.618
29	LYS	HZ1	7.615
29	LYS	HZ2	7.615
29	LYS	HZ3	7.615

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	192	191	99.5
¹³C chemical shifts	143	92	64.3
¹⁵N chemical shifts	32	31	96.9

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	63	62	98.4
¹³C chemical shifts	60	26	43.3
¹⁵N chemical shifts	29	28	96.6

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	129	129	100.0
¹³C chemical shifts	83	66	79.5
¹⁵N chemical shifts	3	3	100.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	14	14	100.0
¹³C chemical shifts	14	14	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	21	21	100.0
¹³C chemical shifts	20	20	100.0
¹⁵N chemical shifts	1	1	100.0

Peptide bond of PRO
Tautomeric state of HIS
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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_4
- 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: 534
- Weight of restraints: 1.0 (534)
- Potential type of restraints: upper-bound-parabolic (534)
- Range of distance target values: 2.62, 5.5 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 80.0%
- Total number of restraints: 36
- Total number of restraints per polymer type: 36
- Weight of restraints: 1.0 (36)
- Potential type of restraints: square-well-parabolic (36)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Bacteriocin, helix, LsbB, TFE Water