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BMRB: 16148

2KEG

NMR structure of Plantaricin K in DPC-micelles

Authors

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

Assembly

PlnK

Entity

1. PlnK (polymer, Thiol state: not present), 32 monomers, 3502.901 Da Detail

RRSRKNGIGY AIGYAFGAVE RAVLGGSRDY NK

Formula weight

3502.901 Da

Source organism

Lactiplantibacillus plantarum

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 74.2 %, Completeness (bb): 74.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	74.2 % (267 of 360)	94.7 % (179 of 189)	40.9 % (56 of 137)	94.1 % (32 of 34)
Backbone	74.5 % (143 of 192)	94.3 % (66 of 70)	50.0 % (45 of 90)	100.0 % (32 of 32)
Sidechain	73.2 % (142 of 194)	95.0 % (113 of 119)	39.7 % (29 of 73)	0.0 % (0 of 2)
Aromatic	52.9 % (18 of 34)	94.1 % (16 of 17)	11.8 % (2 of 17)
Methyl	75.0 % (21 of 28)	100.0 % (14 of 14)	50.0 % (7 of 14)

1. PlnK

RRSRKNGIGY AIGYAFGAVE RAVLGGSRDY NK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 312 K, pH 2.5, Details PlnK in DPC-micelles

#	Name	Isotope labeling	Type	Concentration
1	PlnK	natural abundance		1 mM
2	DPC	[U-99% 2H]		170 mM
3	TFA	natural abundance		0.1 %
4	D2O	natural abundance		10 %
5	H2O	natural abundance		90 %
6	DSS	natural abundance		0.2 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2KEG, Strand ID: A 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. PlnK, : 1 : 1 : 4 entities Detail

Experiments performed 6 experiments Detail

1 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz Avance II UiO Bruker Avance II University of Oslo Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 312 K, pH 2.5, Details PlnK in DPC-micelles

#	Name	Isotope labeling	Type	Concentration
1	PlnK	natural abundance		1 mM
2	DPC	[U-99% 2H]		170 mM
3	TFA	natural abundance		0.1 %
4	D2O	natural abundance		10 %
5	H2O	natural abundance		90 %
6	DSS	natural abundance		0.2 mM

2 2D 1H-1H COSY

Instrument

Bruker Avance - 600 MHz Avance II UiO Bruker Avance II University of Oslo Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 312 K, pH 2.5, Details PlnK in DPC-micelles

#	Name	Isotope labeling	Type	Concentration
1	PlnK	natural abundance		1 mM
2	DPC	[U-99% 2H]		170 mM
3	TFA	natural abundance		0.1 %
4	D2O	natural abundance		10 %
5	H2O	natural abundance		90 %
6	DSS	natural abundance		0.2 mM

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz Avance II UiO Bruker Avance II University of Oslo Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 312 K, pH 2.5, Details PlnK in DPC-micelles

#	Name	Isotope labeling	Type	Concentration
1	PlnK	natural abundance		1 mM
2	DPC	[U-99% 2H]		170 mM
3	TFA	natural abundance		0.1 %
4	D2O	natural abundance		10 %
5	H2O	natural abundance		90 %
6	DSS	natural abundance		0.2 mM

4 2D DQF-COSY

Instrument

Bruker Avance - 600 MHz Avance II UiO Bruker Avance II University of Oslo Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 312 K, pH 2.5, Details PlnK in DPC-micelles

#	Name	Isotope labeling	Type	Concentration
1	PlnK	natural abundance		1 mM
2	DPC	[U-99% 2H]		170 mM
3	TFA	natural abundance		0.1 %
4	D2O	natural abundance		10 %
5	H2O	natural abundance		90 %
6	DSS	natural abundance		0.2 mM

5 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz Avance II UiO Bruker Avance II University of Oslo Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 312 K, pH 2.5, Details PlnK in DPC-micelles

#	Name	Isotope labeling	Type	Concentration
1	PlnK	natural abundance		1 mM
2	DPC	[U-99% 2H]		170 mM
3	TFA	natural abundance		0.1 %
4	D2O	natural abundance		10 %
5	H2O	natural abundance		90 %
6	DSS	natural abundance		0.2 mM

6 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz Avance II UiO Bruker Avance II University of Oslo Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 312 K, pH 2.5, Details PlnK in DPC-micelles

#	Name	Isotope labeling	Type	Concentration
1	PlnK	natural abundance		1 mM
2	DPC	[U-99% 2H]		170 mM
3	TFA	natural abundance		0.1 %
4	D2O	natural abundance		10 %
5	H2O	natural abundance		90 %
6	DSS	natural abundance		0.2 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16148_2keg.nef
Input source #2: Coordindates	2keg.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--
RRSRKNGIGYAIGYAFGAVERAVLGGSRDYNK
||||||||||||||||||||||||||||||||
RRSRKNGIGYAIGYAFGAVERAVLGGSRDYNK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	32	0	0	100.0

Content subtype: combined_16148_2keg.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	259		100.0 (chain: A, length: 32)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	540 (1)	noe	100.0 (chain: A, length: 32)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	126 (126)	.	68.8 (chain: A, length: 32)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 178
  - ¹³C chemical shifts: 50
  - ¹⁵N chemical shifts: 31
- 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: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 100.0%
- Total number of restraints: 540
- Weight of restraints: 1.0 (540)
- Potential type of restraints: upper-bound-parabolic (540)
- Range of distance target values: 2.36, 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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 68.8%
- Total number of restraints: 126
- Total number of restraints per polymer type: 126
- Weight of restraints: 1.0 (126)
- Potential type of restraints: square-well-parabolic (126)
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Peptide, Protein