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BMRB: 34278

6GNZ

Plantaricin S-a in 100 mM DPC micelles. This is the alpha part of the bacteriocin plantaricin S.

Authors

Ekblad, B., Kristiansen, P.E.

Assembly

Plantaricin S alpha protein

Entity

1. Plantaricin S alpha protein (polymer), 27 monomers, 2922.407 Da Detail

RNKLAYNMGH YAGKATIFGL AAWALLA

Formula weight

2922.407 Da

Source organism

Lactiplantibacillus plantarum

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 80.8 %, Completeness (bb): 68.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.8 % (252 of 312)	99.4 % (157 of 158)	56.5 % (70 of 124)	83.3 % (25 of 30)
Backbone	68.5 % (111 of 162)	100.0 % (57 of 57)	41.0 % (32 of 78)	81.5 % (22 of 27)
Sidechain	93.1 % (162 of 174)	99.0 % (100 of 101)	84.3 % (59 of 70)	100.0 % (3 of 3)
Aromatic	85.7 % (36 of 42)	100.0 % (21 of 21)	70.0 % (14 of 20)	100.0 % (1 of 1)
Methyl	91.7 % (33 of 36)	100.0 % (18 of 18)	83.3 % (15 of 18)

1. Plantaricin S alpha protein

RNKLAYNMGH YAGKATIFGL AAWALLA

Show sample condition

Sample

Solvent system 95%, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM Plantaricin Sb, 0.2 mM DSS, 100 mM [U-100% 2H] DPC, 95%

#	Name	Isotope labeling	Type	Concentration
1	Plantaricin Sb	natural abundance		1 (±0.05) mM
2	DSS	natural abundance		0.2 (±0.01) mM
3	DPC	[U-100% 2H]		100 (±0.05) mM

Protein Blocks Logo

Calculated from 20 models in PDB: 6GNZ, 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 alpha protein, : 1 entities Detail

Experiments performed 6 experiments Detail

1 1D proton

Instrument

Bruker AvanceII - 600 MHz with cryoprobe

Sample

State anisotropic, Solvent system 95%, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM Plantaricin Sb, 0.2 mM DSS, 100 mM [U-100% 2H] DPC, 95%

#	Name	Isotope labeling	Type	Concentration
1	Plantaricin Sb	natural abundance		1 (±0.05) mM
2	DSS	natural abundance		0.2 (±0.01) mM
3	DPC	[U-100% 2H]		100 (±0.05) mM

2 2D NOESY

Instrument

Bruker AvanceII - 600 MHz with cryoprobe

Sample

State anisotropic, Solvent system 95%, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM Plantaricin Sb, 0.2 mM DSS, 100 mM [U-100% 2H] DPC, 95%

#	Name	Isotope labeling	Type	Concentration
1	Plantaricin Sb	natural abundance		1 (±0.05) mM
2	DSS	natural abundance		0.2 (±0.01) mM
3	DPC	[U-100% 2H]		100 (±0.05) mM

3 2D DQF-COSY

Instrument

Bruker AvanceII - 600 MHz with cryoprobe

Sample

State anisotropic, Solvent system 95%, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM Plantaricin Sb, 0.2 mM DSS, 100 mM [U-100% 2H] DPC, 95%

#	Name	Isotope labeling	Type	Concentration
1	Plantaricin Sb	natural abundance		1 (±0.05) mM
2	DSS	natural abundance		0.2 (±0.01) mM
3	DPC	[U-100% 2H]		100 (±0.05) mM

4 2D TOCSY

Instrument

Bruker AvanceII - 600 MHz with cryoprobe

Sample

State anisotropic, Solvent system 95%, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM Plantaricin Sb, 0.2 mM DSS, 100 mM [U-100% 2H] DPC, 95%

#	Name	Isotope labeling	Type	Concentration
1	Plantaricin Sb	natural abundance		1 (±0.05) mM
2	DSS	natural abundance		0.2 (±0.01) mM
3	DPC	[U-100% 2H]		100 (±0.05) mM

5 2D 1H-13C HSQC

Instrument

Bruker AvanceII - 600 MHz with cryoprobe

Sample

State anisotropic, Solvent system 95%, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM Plantaricin Sb, 0.2 mM DSS, 100 mM [U-100% 2H] DPC, 95%

#	Name	Isotope labeling	Type	Concentration
1	Plantaricin Sb	natural abundance		1 (±0.05) mM
2	DSS	natural abundance		0.2 (±0.01) mM
3	DPC	[U-100% 2H]		100 (±0.05) mM

6 2D 1H-15N HSQC

Instrument

Bruker AvanceII - 600 MHz with cryoprobe

Sample

State anisotropic, Solvent system 95%, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM Plantaricin Sb, 0.2 mM DSS, 100 mM [U-100% 2H] DPC, 95%

#	Name	Isotope labeling	Type	Concentration
1	Plantaricin Sb	natural abundance		1 (±0.05) mM
2	DSS	natural abundance		0.2 (±0.01) mM
3	DPC	[U-100% 2H]		100 (±0.05) mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34278_6gnz.nef
Input source #2: Coordindates	6gnz.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-------
RNKLAYNMGHYAGKATIFGLAAWALLA
|||||||||||||||||||||||||||
RNKLAYNMGHYAGKATIFGLAAWALLA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	27	0	0	100.0

Content subtype: combined_34278_6gnz.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	253		100.0 (chain: A, length: 27)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	543 (1)	noe	100.0 (chain: A, length: 27)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	44 (44)	.	88.9 (chain: A, length: 27)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 162
  - ¹³C chemical shifts: 67
  - ¹⁵N chemical shifts: 24
- Completeness of assignments
  - Entity_assemble_ID: A
- 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_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 100.0%
- Total number of restraints: 537
- Weight of restraints: 1.0 (537)
- Potential type of restraints: upper-bound-parabolic (537)
- Range of distance target values: 2.4, 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: 27, Sequence coverage: 88.9%
- Total number of restraints: 44
- Total number of restraints per polymer type: 44
- Weight of restraints: 1.0 (44)
- Potential type of restraints: square-well-parabolic (44)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ANTIMICROBIAL PROTEIN, ANTIMICROBIAL PROTEIN Bacteriocin menbrane interacting peptide