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BMRB: 34279

6GO0

PLANTARICIN S-B IN 100 MM DPC MICELLES. THIS IS THE BETA PART OF THE BACTERIOCIN PLANTARICIN S

Authors

Ekblad, B., Kristiansen, P.E.

Assembly

Plantaricin S beta protein

Entity

1. Plantaricin S beta protein (polymer), 26 monomers, 2873.221 Da Detail

KKKKQSWYAA AGDAIVSFGE GFLNAW

Formula weight

2873.221 Da

Source organism

Lactiplantibacillus plantarum

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 86.9 %, Completeness (bb): 77.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.9 % (271 of 312)	99.4 % (160 of 161)	69.4 % (84 of 121)	90.0 % (27 of 30)
Backbone	77.6 % (121 of 156)	98.2 % (54 of 55)	58.7 % (44 of 75)	88.5 % (23 of 26)
Sidechain	96.1 % (172 of 179)	100.0 % (106 of 106)	89.9 % (62 of 69)	100.0 % (4 of 4)
Aromatic	88.5 % (46 of 52)	100.0 % (26 of 26)	75.0 % (18 of 24)	100.0 % (2 of 2)
Methyl	100.0 % (22 of 22)	100.0 % (11 of 11)	100.0 % (11 of 11)

1. Plantaricin S beta protein

KKKKQSWYAA AGDAIVSFGE GFLNAW

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.2) K, pH 6.5, Details 1 mM Plantaricin S-b, 95 % H2O, 5 % [U-2H] D2O, 100 mM [U-2H] DPC, 0.2 mM DSS, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Plantaricin S-b	natural abundance		1 (±0.1) mM
2	H2O	natural abundance		95 (±0.1) %
3	D2O	[U-2H]		5 (±0.1) %
4	DPC	[U-2H]		100 (±5.0) mM
5	DSS	natural abundance		0.2 (±0.01) mM

Protein Blocks Logo

Calculated from 20 models in PDB: 6GO0, Strand ID: A Detail

Release date

2018-06-17

Citation

NMR structures and mutational analysis of the two peptides constituting the bacteriocin plantaricin S
Ekblad, B., Kristiansen, P.E.
Sci. Rep. (2019), 9, 2333-2333, PubMed 30787405 , DOI 10.1038/s41598-019-38518-6 , Abstract

Related entities 1. Plantaricin S beta protein, : 1 : 2 entities Detail

Experiments performed 6 experiments Detail

1 1D proton

Instrument

Bruker AvanceII - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.2) K, pH 6.5, Details 1 mM Plantaricin S-b, 95 % H2O, 5 % [U-2H] D2O, 100 mM [U-2H] DPC, 0.2 mM DSS, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Plantaricin S-b	natural abundance		1 (±0.1) mM
2	H2O	natural abundance		95 (±0.1) %
3	D2O	[U-2H]		5 (±0.1) %
4	DPC	[U-2H]		100 (±5.0) mM
5	DSS	natural abundance		0.2 (±0.01) mM

2 2D DQF-COSY

Instrument

Bruker AvanceII - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.2) K, pH 6.5, Details 1 mM Plantaricin S-b, 95 % H2O, 5 % [U-2H] D2O, 100 mM [U-2H] DPC, 0.2 mM DSS, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Plantaricin S-b	natural abundance		1 (±0.1) mM
2	H2O	natural abundance		95 (±0.1) %
3	D2O	[U-2H]		5 (±0.1) %
4	DPC	[U-2H]		100 (±5.0) mM
5	DSS	natural abundance		0.2 (±0.01) mM

3 2D 1H-1H TOCSY

Instrument

Bruker AvanceII - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.2) K, pH 6.5, Details 1 mM Plantaricin S-b, 95 % H2O, 5 % [U-2H] D2O, 100 mM [U-2H] DPC, 0.2 mM DSS, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Plantaricin S-b	natural abundance		1 (±0.1) mM
2	H2O	natural abundance		95 (±0.1) %
3	D2O	[U-2H]		5 (±0.1) %
4	DPC	[U-2H]		100 (±5.0) mM
5	DSS	natural abundance		0.2 (±0.01) mM

4 2D 1H-1H NOESY

Instrument

Bruker AvanceII - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.2) K, pH 6.5, Details 1 mM Plantaricin S-b, 95 % H2O, 5 % [U-2H] D2O, 100 mM [U-2H] DPC, 0.2 mM DSS, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Plantaricin S-b	natural abundance		1 (±0.1) mM
2	H2O	natural abundance		95 (±0.1) %
3	D2O	[U-2H]		5 (±0.1) %
4	DPC	[U-2H]		100 (±5.0) mM
5	DSS	natural abundance		0.2 (±0.01) mM

5 2D 1H-13C HSQC

Instrument

Bruker AvanceII - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.2) K, pH 6.5, Details 1 mM Plantaricin S-b, 95 % H2O, 5 % [U-2H] D2O, 100 mM [U-2H] DPC, 0.2 mM DSS, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Plantaricin S-b	natural abundance		1 (±0.1) mM
2	H2O	natural abundance		95 (±0.1) %
3	D2O	[U-2H]		5 (±0.1) %
4	DPC	[U-2H]		100 (±5.0) mM
5	DSS	natural abundance		0.2 (±0.01) mM

6 2D 1H-15N HSQC

Instrument

Bruker AvanceII - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.2) K, pH 6.5, Details 1 mM Plantaricin S-b, 95 % H2O, 5 % [U-2H] D2O, 100 mM [U-2H] DPC, 0.2 mM DSS, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Plantaricin S-b	natural abundance		1 (±0.1) mM
2	H2O	natural abundance		95 (±0.1) %
3	D2O	[U-2H]		5 (±0.1) %
4	DPC	[U-2H]		100 (±5.0) mM
5	DSS	natural abundance		0.2 (±0.01) mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_34279_6go0.nef
Input source #2: Coordindates	6go0.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------
KKKKQSWYAAAGDAIVSFGEGFLNAW
||||||||||||||||||||||||||
KKKKQSWYAAAGDAIVSFGEGFLNAW

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	26	0	0	100.0

Content subtype: combined_34279_6go0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	272		100.0 (chain: A, length: 26)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	807 (1)	noe	100.0 (chain: A, length: 26)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 26, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 163
  - ¹³C chemical shifts: 82
  - ¹⁵N chemical shifts: 27
- 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: 26, Sequence coverage: 100.0%
- Total number of restraints: 801
- Weight of restraints: 1.0 (801)
- Potential type of restraints: upper-bound-parabolic (801)
- Range of distance target values: 2.44, 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 ANTIMICROBIAL PROTEIN, ANTIMICROBIAL PROTEIN Bacteriocin menbrane interacting peptide