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BMRB: 16241

2KHG

Plantaricin J in TFE

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: 88.5 %, Completeness (bb): 80.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.5 % (270 of 305)	99.4 % (160 of 161)	73.3 % (85 of 116)	89.3 % (25 of 28)
Backbone	80.7 % (121 of 150)	98.1 % (53 of 54)	64.8 % (46 of 71)	88.0 % (22 of 25)
Sidechain	96.6 % (170 of 176)	100.0 % (107 of 107)	90.9 % (60 of 66)	100.0 % (3 of 3)
Aromatic	88.5 % (46 of 52)	100.0 % (26 of 26)	75.0 % (18 of 24)	100.0 % (2 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

Solvent system trifluoroethanol/water, Pressure 1 atm, Temperature 297 K, pH 2.5, Details Unlabeled PlnJ in DPC-micelles

#	Name	Isotope labeling	Type	Concentration
1	PlnJ	natural abundance		1 mM
2	TFE	[U-99% 2H]		50 %
3	TFA	natural abundance		0.1 %
4	DSS	natural abundance		0.2 mM

Protein Blocks Logo

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

Coupling constant

19 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 6 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 trifluoroethanol/water, Pressure 1 atm, Temperature 297 K, pH 2.5, Details Unlabeled PlnJ in DPC-micelles

#	Name	Isotope labeling	Type	Concentration
1	PlnJ	natural abundance		1 mM
2	TFE	[U-99% 2H]		50 %
3	TFA	natural abundance		0.1 %
4	DSS	natural abundance		0.2 mM

2 2D 1H-13C HSQC

Instrument

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

Sample

State isotropic, Solvent system trifluoroethanol/water, Pressure 1 atm, Temperature 297 K, pH 2.5, Details Unlabeled PlnJ in DPC-micelles

#	Name	Isotope labeling	Type	Concentration
1	PlnJ	natural abundance		1 mM
2	TFE	[U-99% 2H]		50 %
3	TFA	natural abundance		0.1 %
4	DSS	natural abundance		0.2 mM

3 2D 1H-1H COSY

Instrument

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

Sample

State isotropic, Solvent system trifluoroethanol/water, Pressure 1 atm, Temperature 297 K, pH 2.5, Details Unlabeled PlnJ in DPC-micelles

#	Name	Isotope labeling	Type	Concentration
1	PlnJ	natural abundance		1 mM
2	TFE	[U-99% 2H]		50 %
3	TFA	natural abundance		0.1 %
4	DSS	natural abundance		0.2 mM

4 2D DQF-COSY

Instrument

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

Sample

State isotropic, Solvent system trifluoroethanol/water, Pressure 1 atm, Temperature 297 K, pH 2.5, Details Unlabeled PlnJ in DPC-micelles

#	Name	Isotope labeling	Type	Concentration
1	PlnJ	natural abundance		1 mM
2	TFE	[U-99% 2H]		50 %
3	TFA	natural abundance		0.1 %
4	DSS	natural abundance		0.2 mM

5 2D 1H-1H TOCSY

Instrument

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

Sample

State isotropic, Solvent system trifluoroethanol/water, Pressure 1 atm, Temperature 297 K, pH 2.5, Details Unlabeled PlnJ in DPC-micelles

#	Name	Isotope labeling	Type	Concentration
1	PlnJ	natural abundance		1 mM
2	TFE	[U-99% 2H]		50 %
3	TFA	natural abundance		0.1 %
4	DSS	natural abundance		0.2 mM

6 2D 1H-1H NOESY

Instrument

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

Sample

State isotropic, Solvent system trifluoroethanol/water, Pressure 1 atm, Temperature 297 K, pH 2.5, Details Unlabeled PlnJ in DPC-micelles

#	Name	Isotope labeling	Type	Concentration
1	PlnJ	natural abundance		1 mM
2	TFE	[U-99% 2H]		50 %
3	TFA	natural abundance		0.1 %
4	DSS	natural abundance		0.2 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16241_2khg.nef
Input source #2: Coordindates	2khg.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
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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_16241_2khg.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	291		100.0 (chain: A, length: 25)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	455 (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%

--------10--------20-----
GAWKNFWSSLRKGFYDGEAGRAIRR
|||||||||||||||||||||||||
GAWKNFWSSLRKGFYDGEAGRAIRR

Total number of assignments
- ¹H chemical shifts: 176
- ¹³C chemical shifts: 88
- ¹⁵N chemical shifts: 27

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
3	TRP	CD2	129.718
3	TRP	CE2	139.355
3	TRP	CG	111.469
4	LYS	HZ1	7.654
4	LYS	HZ2	7.654
4	LYS	HZ3	7.654
6	PHE	CG	137.225
7	TRP	CE2	139.345
12	LYS	HZ1	7.588
12	LYS	HZ2	7.588
12	LYS	HZ3	7.588
15	TYR	CG	130.919
15	TYR	CZ	157.61

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	161	160	99.4
¹³C chemical shifts	116	81	69.8
¹⁵N chemical shifts	32	27	84.4

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	53	98.1
¹³C chemical shifts	50	21	42.0
¹⁵N chemical shifts	25	22	88.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	107	107	100.0
¹³C chemical shifts	66	60	90.9
¹⁵N chemical shifts	7	5	71.4

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	7	100.0
¹³C chemical shifts	7	7	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	26	100.0
¹³C chemical shifts	24	18	75.0
¹⁵N chemical shifts	2	2	100.0

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: 451
- Weight of restraints: 1.0 (451)
- Potential type of restraints: upper-bound-parabolic (451)
- Range of distance target values: 2.7, 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