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BMRB: 16239

2KHF

Plantaricin J in DPC-micelles

Authors

Rogne, P., Haugen, C., Kristiansen, P., Nissen-Meyer, J.

Assembly

Plantaricin J

Entity

1. Plantaricin J (polymer, Thiol state: not present), 25 monomers, 2929.258 Da Detail

GAWKNFWSSL RKGFYDGEAG RAIRR

Formula weight

2929.258 Da

Source organism

Lactiplantibacillus plantarum

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts, coupling_constants

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 86.6 %, Completeness (bb): 78.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.6 % (264 of 305)	99.4 % (160 of 161)	69.0 % (80 of 116)	85.7 % (24 of 28)
Backbone	78.7 % (118 of 150)	98.1 % (53 of 54)	59.2 % (42 of 71)	92.0 % (23 of 25)
Sidechain	94.9 % (167 of 176)	100.0 % (107 of 107)	89.4 % (59 of 66)	33.3 % (1 of 3)
Aromatic	84.6 % (44 of 52)	100.0 % (26 of 26)	75.0 % (18 of 24)	0.0 % (0 of 2)
Methyl	100.0 % (14 of 14)	100.0 % (7 of 7)	100.0 % (7 of 7)

1. PlnJ

GAWKNFWSSL RKGFYDGEAG RAIRR

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 2.5, Details 15N-Labeled PlnJ

#	Name	Isotope labeling	Type	Concentration
1	PlnJ	[U-95% 15N]		0.6 mM
2	DPC	[U-99% 2H]		100 mM
3	DSS	natural abundance		0.2 mM
4	D2O	[U-2H]		10 %
5	TFA	natural abundance		0.1 %
6	H2O	natural abundance		90 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 2.5, Details Unlabeled PlnJ in DPC-micelles

#	Name	Isotope labeling	Type	Concentration
7	PlnJ	natural abundance		1 mM
8	DPC	[U-99% 2H]		170 mM
9	TFA	natural abundance		0.1 %
10	DSS	natural abundance		0.2 mM
11	D2O	[U-2H]		10 %
12	H2O	natural abundance		90 %

Protein Blocks Logo

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

Coupling constant

18 J values in 1 lists
Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 297 K, pH 2.5 Detail

Release date

2009-06-24

Citation

Three-dimensional structure of the two-peptide bacteriocin plantaricin JK
Rogne, P., Haugen, C., Fimland, G., Nissen-Meyer, J., Kristiansen, P.
Peptides (2009), 30, 1613-1621, PubMed 19538999 , DOI 10.1016/j.peptides.2009.06.010 , Abstract

Related entities 1. Plantaricin J, : 1 : 1 entities Detail

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz Biomolecular NMR Bruker Avance II Universtity of Oslo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 2.5, Details 15N-Labeled PlnJ

#	Name	Isotope labeling	Type	Concentration
1	PlnJ	[U-95% 15N]		0.6 mM
2	DPC	[U-99% 2H]		100 mM
3	DSS	natural abundance		0.2 mM
4	D2O	[U-2H]		10 %
5	TFA	natural abundance		0.1 %
6	H2O	natural abundance		90 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz Biomolecular NMR Bruker Avance II Universtity of Oslo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 2.5, Details 15N-Labeled PlnJ

#	Name	Isotope labeling	Type	Concentration
1	PlnJ	[U-95% 15N]		0.6 mM
2	DPC	[U-99% 2H]		100 mM
3	DSS	natural abundance		0.2 mM
4	D2O	[U-2H]		10 %
5	TFA	natural abundance		0.1 %
6	H2O	natural abundance		90 %

3 2D 1H-1H COSY

Instrument

Bruker Avance - 600 MHz Biomolecular NMR Bruker Avance II Universtity of Oslo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 2.5, Details 15N-Labeled PlnJ

#	Name	Isotope labeling	Type	Concentration
1	PlnJ	[U-95% 15N]		0.6 mM
2	DPC	[U-99% 2H]		100 mM
3	DSS	natural abundance		0.2 mM
4	D2O	[U-2H]		10 %
5	TFA	natural abundance		0.1 %
6	H2O	natural abundance		90 %

4 2D DQF-COSY

Instrument

Bruker Avance - 600 MHz Biomolecular NMR Bruker Avance II Universtity of Oslo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 2.5, Details 15N-Labeled PlnJ

#	Name	Isotope labeling	Type	Concentration
1	PlnJ	[U-95% 15N]		0.6 mM
2	DPC	[U-99% 2H]		100 mM
3	DSS	natural abundance		0.2 mM
4	D2O	[U-2H]		10 %
5	TFA	natural abundance		0.1 %
6	H2O	natural abundance		90 %

5 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz Biomolecular NMR Bruker Avance II Universtity of Oslo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 2.5, Details 15N-Labeled PlnJ

#	Name	Isotope labeling	Type	Concentration
1	PlnJ	[U-95% 15N]		0.6 mM
2	DPC	[U-99% 2H]		100 mM
3	DSS	natural abundance		0.2 mM
4	D2O	[U-2H]		10 %
5	TFA	natural abundance		0.1 %
6	H2O	natural abundance		90 %

6 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz Biomolecular NMR Bruker Avance II Universtity of Oslo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 2.5, Details 15N-Labeled PlnJ

#	Name	Isotope labeling	Type	Concentration
1	PlnJ	[U-95% 15N]		0.6 mM
2	DPC	[U-99% 2H]		100 mM
3	DSS	natural abundance		0.2 mM
4	D2O	[U-2H]		10 %
5	TFA	natural abundance		0.1 %
6	H2O	natural abundance		90 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz Biomolecular NMR Bruker Avance II Universtity of Oslo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 2.5, Details 15N-Labeled PlnJ

#	Name	Isotope labeling	Type	Concentration
1	PlnJ	[U-95% 15N]		0.6 mM
2	DPC	[U-99% 2H]		100 mM
3	DSS	natural abundance		0.2 mM
4	D2O	[U-2H]		10 %
5	TFA	natural abundance		0.1 %
6	H2O	natural abundance		90 %

8 3D 1H-15N TOCSY

Instrument

Bruker Avance - 600 MHz Biomolecular NMR Bruker Avance II Universtity of Oslo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 2.5, Details 15N-Labeled PlnJ

#	Name	Isotope labeling	Type	Concentration
1	PlnJ	[U-95% 15N]		0.6 mM
2	DPC	[U-99% 2H]		100 mM
3	DSS	natural abundance		0.2 mM
4	D2O	[U-2H]		10 %
5	TFA	natural abundance		0.1 %
6	H2O	natural abundance		90 %

9 3D HNHA

Instrument

Bruker Avance - 600 MHz Biomolecular NMR Bruker Avance II Universtity of Oslo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 2.5, Details 15N-Labeled PlnJ

#	Name	Isotope labeling	Type	Concentration
1	PlnJ	[U-95% 15N]		0.6 mM
2	DPC	[U-99% 2H]		100 mM
3	DSS	natural abundance		0.2 mM
4	D2O	[U-2H]		10 %
5	TFA	natural abundance		0.1 %
6	H2O	natural abundance		90 %

10 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz Biomolecular NMR Bruker Avance II Universtity of Oslo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 2.5, Details Unlabeled PlnJ in DPC-micelles

#	Name	Isotope labeling	Type	Concentration
7	PlnJ	natural abundance		1 mM
8	DPC	[U-99% 2H]		170 mM
9	TFA	natural abundance		0.1 %
10	DSS	natural abundance		0.2 mM
11	D2O	[U-2H]		10 %
12	H2O	natural abundance		90 %

11 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz Biomolecular NMR Bruker Avance II Universtity of Oslo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 2.5, Details Unlabeled PlnJ in DPC-micelles

#	Name	Isotope labeling	Type	Concentration
7	PlnJ	natural abundance		1 mM
8	DPC	[U-99% 2H]		170 mM
9	TFA	natural abundance		0.1 %
10	DSS	natural abundance		0.2 mM
11	D2O	[U-2H]		10 %
12	H2O	natural abundance		90 %

12 2D 1H-1H COSY

Instrument

Bruker Avance - 600 MHz Biomolecular NMR Bruker Avance II Universtity of Oslo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 2.5, Details Unlabeled PlnJ in DPC-micelles

#	Name	Isotope labeling	Type	Concentration
7	PlnJ	natural abundance		1 mM
8	DPC	[U-99% 2H]		170 mM
9	TFA	natural abundance		0.1 %
10	DSS	natural abundance		0.2 mM
11	D2O	[U-2H]		10 %
12	H2O	natural abundance		90 %

13 2D DQF-COSY

Instrument

Bruker Avance - 600 MHz Biomolecular NMR Bruker Avance II Universtity of Oslo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 2.5, Details Unlabeled PlnJ in DPC-micelles

#	Name	Isotope labeling	Type	Concentration
7	PlnJ	natural abundance		1 mM
8	DPC	[U-99% 2H]		170 mM
9	TFA	natural abundance		0.1 %
10	DSS	natural abundance		0.2 mM
11	D2O	[U-2H]		10 %
12	H2O	natural abundance		90 %

14 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz Biomolecular NMR Bruker Avance II Universtity of Oslo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 2.5, Details Unlabeled PlnJ in DPC-micelles

#	Name	Isotope labeling	Type	Concentration
7	PlnJ	natural abundance		1 mM
8	DPC	[U-99% 2H]		170 mM
9	TFA	natural abundance		0.1 %
10	DSS	natural abundance		0.2 mM
11	D2O	[U-2H]		10 %
12	H2O	natural abundance		90 %

15 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz Biomolecular NMR Bruker Avance II Universtity of Oslo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 2.5, Details Unlabeled PlnJ in DPC-micelles

#	Name	Isotope labeling	Type	Concentration
7	PlnJ	natural abundance		1 mM
8	DPC	[U-99% 2H]		170 mM
9	TFA	natural abundance		0.1 %
10	DSS	natural abundance		0.2 mM
11	D2O	[U-2H]		10 %
12	H2O	natural abundance		90 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16239_2khf.nef
Input source #2: Coordindates	2khf.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-----
GAWKNFWSSLRKGFYDGEAGRAIRR
|||||||||||||||||||||||||
GAWKNFWSSLRKGFYDGEAGRAIRR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	25	0	0	100.0

Content subtype: combined_16239_2khf.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	280		100.0 (chain: A, length: 25)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	563 (1)	noe	100.0 (chain: A, length: 25)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 25, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 176
  - ¹³C chemical shifts: 80
  - ¹⁵N chemical shifts: 24
- Completeness of assignments
  - Entity_assemble_ID: A
- 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_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 25, Sequence coverage: 100.0%
- Total number of restraints: 562
- Weight of restraints: 1.0 (562)
- Potential type of restraints: upper-bound-parabolic (562)
- Range of distance target values: 2.41, 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

Keywords Anti-microbial peptides, Bacteriocins, Lactic acid bacteria, NMR-spectroscopy, Peptide structure, Plantaricin JK, Anti-microbial, Bacteriocin, Peptide, Two-peptide