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BMRB: 34018

5LFI

Lactococcin A immunity protein

Authors

Persson, C., Fuochi, V., Pedersen, A., Karlsson, B.G., Nissen-Meyer, J., Kristiansen, P.E., Oppegard, C.

Assembly

Lactococcin-A immunity protein

Entity

1. Lactococcin-A immunity protein (polymer, Thiol state: not present), 117 monomers, 13249.00 Da Detail

MSGSHHHHHH SSGIEGRGRM KKKQIEFENE LRSMLATALE KDISQEERNA LNIAEKALDN SEYLPKIILN LRKALTPLAI NRTLNHDLSE LYKFITSSKA SNKNLGGGLI MSWGRLF

Formula weight

13249.0 Da

Source organism

Lactococcus lactis subsp. lactis

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 84.6 %, Completeness: 71.8 %, Completeness (bb): 77.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	71.8 % (997 of 1388)	67.8 % (494 of 729)	75.8 % (403 of 532)	78.7 % (100 of 127)
Backbone	77.9 % (544 of 698)	73.8 % (177 of 240)	80.2 % (275 of 343)	80.0 % (92 of 115)
Sidechain	67.8 % (542 of 799)	64.8 % (317 of 489)	72.8 % (217 of 298)	66.7 % (8 of 12)
Aromatic	50.0 % (43 of 86)	51.2 % (22 of 43)	47.6 % (20 of 42)	100.0 % (1 of 1)
Methyl	90.3 % (112 of 124)	90.3 % (56 of 62)	90.3 % (56 of 62)

1. entity 1

MSGSHHHHHH SSGIEGRGRM KKKQIEFENE LRSMLATALE KDISQEERNA LNIAEKALDN SEYLPKIILN LRKALTPLAI NRTLNHDLSE LYKFITSSKA SNKNLGGGLI MSWGRLF

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.5 mM [U-100% 13C; U-100% 15N] lactococcin A immunity protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	lactococcin A immunity protein	[U-100% 13C; U-100% 15N]		0.5 mM

LACS Plot; CA

Referencing offset: -0.07 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.07 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.09 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.22 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 16 models in PDB: 5LFI, Strand ID: A Detail

Release date

2016-11-13

Citation

Nuclear Magnetic Resonance Structure and Mutational Analysis of the Lactococcin A Immunity Protein
Kristiansen, P.E., Persson, C., Fuochi, V., Pedersen, A., Karlsson, G.B., Nissen-Meyer, J., Oppegard, C.
Biochemistry (2016), 55, 6250-6257, PubMed 27808503 , DOI 10.1021/acs.biochem.6b00848 , Abstract

Related entities 1. Lactococcin-A immunity protein, : 1 : 1 entities Detail

Interaction partners 1. Lactococcin-A immunity protein, : 2 interactors Detail

More details for 2 interactors identified by 1 citations

Experiments performed 14 experiments Detail

1 3D HNCO

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.5 mM [U-100% 13C; U-100% 15N] lactococcin A immunity protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	lactococcin A immunity protein	[U-100% 13C; U-100% 15N]		0.5 mM

2 3D HNCA

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.5 mM [U-100% 13C; U-100% 15N] lactococcin A immunity protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	lactococcin A immunity protein	[U-100% 13C; U-100% 15N]		0.5 mM

3 3D HNCACB

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.5 mM [U-100% 13C; U-100% 15N] lactococcin A immunity protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	lactococcin A immunity protein	[U-100% 13C; U-100% 15N]		0.5 mM

4 3D HN(CO)CA

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.5 mM [U-100% 13C; U-100% 15N] lactococcin A immunity protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	lactococcin A immunity protein	[U-100% 13C; U-100% 15N]		0.5 mM

5 3D HN(COCA)CB

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.5 mM [U-100% 13C; U-100% 15N] lactococcin A immunity protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	lactococcin A immunity protein	[U-100% 13C; U-100% 15N]		0.5 mM

6 3D HN(CA)CO

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.5 mM [U-100% 13C; U-100% 15N] lactococcin A immunity protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	lactococcin A immunity protein	[U-100% 13C; U-100% 15N]		0.5 mM

7 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.5 mM [U-100% 13C; U-100% 15N] lactococcin A immunity protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	lactococcin A immunity protein	[U-100% 13C; U-100% 15N]		0.5 mM

8 3D 1H-15N TOCSY

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.5 mM [U-100% 13C; U-100% 15N] lactococcin A immunity protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	lactococcin A immunity protein	[U-100% 13C; U-100% 15N]		0.5 mM

9 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.5 mM [U-100% 13C; U-100% 15N] lactococcin A immunity protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	lactococcin A immunity protein	[U-100% 13C; U-100% 15N]		0.5 mM

10 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.5 mM [U-100% 13C; U-100% 15N] lactococcin A immunity protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	lactococcin A immunity protein	[U-100% 13C; U-100% 15N]		0.5 mM

11 3D 1H-13C NOESY aromatic

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.5 mM [U-100% 13C; U-100% 15N] lactococcin A immunity protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	lactococcin A immunity protein	[U-100% 13C; U-100% 15N]		0.5 mM

12 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.5 mM [U-100% 13C; U-100% 15N] lactococcin A immunity protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	lactococcin A immunity protein	[U-100% 13C; U-100% 15N]		0.5 mM

13 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.5 mM [U-100% 13C; U-100% 15N] lactococcin A immunity protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	lactococcin A immunity protein	[U-100% 13C; U-100% 15N]		0.5 mM

14 2D 1H-13C HSQC aromatic

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.5 mM [U-100% 13C; U-100% 15N] lactococcin A immunity protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	lactococcin A immunity protein	[U-100% 13C; U-100% 15N]		0.5 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34018_5lfi.nef
Input source #2: Coordindates	5lfi.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--------40--------50--------60--------70--------80--------90-------100
MSGSHHHHHHSSGIEGRGRMKKKQIEFENELRSMLATALEKDISQEERNALNIAEKALDNSEYLPKIILNLRKALTPLAINRTLNHDLSELYKFITSSKA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSGSHHHHHHSSGIEGRGRMKKKQIEFENELRSMLATALEKDISQEERNALNIAEKALDNSEYLPKIILNLRKALTPLAINRTLNHDLSELYKFITSSKA

-------110-------
SNKNLGGGLIMSWGRLF
|||||||||||||||||
SNKNLGGGLIMSWGRLF

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	117	0	0	100.0

Content subtype: combined_34018_5lfi.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	968		83.8 (chain: A, length: 117)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	1835 (1)	noe	66.7 (chain: A, length: 117)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	136 (136)	.	66.7 (chain: A, length: 117)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 117, Sequence coverage: 83.8%
- Total number of assignments
  - ¹³C chemical shifts: 394
  - ¹H chemical shifts: 476
  - ¹⁵N chemical shifts: 98
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- 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_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 117, Sequence coverage: 66.7%
- Total number of restraints: 1830
- Weight of restraints: 1.0 (1830)
- Potential type of restraints: upper-bound-parabolic (1830)
- Range of distance target values: 2.6, 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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 117, Sequence coverage: 66.7%
- Total number of restraints: 136
- Total number of restraints per polymer type: 136
- Weight of restraints: 1.0 (136)
- Potential type of restraints: square-well-parabolic (136)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Four-helix bundle, Immune system, bacteriocin receptor, immunity protein