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BMRB: 34044

5LWC

Solution structure of bacteriocin BacSp222 from Staphylococcus pseudintermedius 222

Authors

Nowakowski, M.E., Ejchart, A.O., Jaremko, L., Wladyka, B., Mak, P.

Assembly

Bacteriocin BacSp222

Entity

1. Bacteriocin BacSp222 (polymer), 50 monomers, 5920.800 Da Detail

XAGLLRFLLS KGRALYNWAK SHVGKVWEWL KSGATYEQIK EWIENALGWR

Formula weight

5920.8 Da

Source organism

Staphylococcus pseudintermedius

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.0 %, Completeness: 92.7 %, Completeness (bb): 96.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.7 % (573 of 618)	91.6 % (294 of 321)	93.8 % (225 of 240)	94.7 % (54 of 57)
Backbone	96.3 % (283 of 294)	96.1 % (99 of 103)	95.1 % (135 of 142)	100.0 % (49 of 49)
Sidechain	90.8 % (334 of 368)	89.4 % (195 of 218)	94.4 % (134 of 142)	62.5 % (5 of 8)
Aromatic	83.3 % (75 of 90)	82.2 % (37 of 45)	82.5 % (33 of 40)	100.0 % (5 of 5)
Methyl	98.2 % (55 of 56)	96.4 % (27 of 28)	100.0 % (28 of 28)

1. Bacteriocin BacSp222

XAGLLRFLLS KGRALYNWAK SHVGKVWEWL KSGATYEQIK EWIENALGWR

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 5, Details 0.5 mM [U-99% 13C; U-99% 15N] BacSp222, 100 mM [U-100% 2H] sodium acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	BacSp222	[U-99% 13C; U-99% 15N]		0.5 mM
2	sodium acetate	[U-100% 2H]		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 5LWC, Strand ID: A Detail

Release date

2016-09-19

Citation

Spatial attributes of the four-helix bundle group of bacteriocins-the high-resolution structure of BacSp222 in solution
Nowakowski, M., Jaremko, L., Wladyka, B., Dubin, G., Ejchart, A., Mak, P.
Int. J. Biol. Macromol. (2017), 33063-33065, PubMed 29107139 , DOI 10.1016/j.ijbiomac.2017.10.158 , Abstract

Related entities 1. Bacteriocin BacSp222, : 1 entities Detail

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian Uniform NMR System - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 5, Details 0.5 mM [U-99% 13C; U-99% 15N] BacSp222, 100 mM [U-100% 2H] sodium acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	BacSp222	[U-99% 13C; U-99% 15N]		0.5 mM
2	sodium acetate	[U-100% 2H]		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

2 2D 1H-13C HSQC aliphatic

Instrument

Varian Uniform NMR System - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 5, Details 0.5 mM [U-99% 13C; U-99% 15N] BacSp222, 100 mM [U-100% 2H] sodium acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	BacSp222	[U-99% 13C; U-99% 15N]		0.5 mM
2	sodium acetate	[U-100% 2H]		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

3 2D 1H-13C HSQC aromatic

Instrument

Varian Uniform NMR System - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 5, Details 0.5 mM [U-99% 13C; U-99% 15N] BacSp222, 100 mM [U-100% 2H] sodium acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	BacSp222	[U-99% 13C; U-99% 15N]		0.5 mM
2	sodium acetate	[U-100% 2H]		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

4 3D HNCO

Instrument

Varian Uniform NMR System - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 5, Details 0.5 mM [U-99% 13C; U-99% 15N] BacSp222, 100 mM [U-100% 2H] sodium acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	BacSp222	[U-99% 13C; U-99% 15N]		0.5 mM
2	sodium acetate	[U-100% 2H]		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

5 3D C(CO)NH

Instrument

Varian Uniform NMR System - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 5, Details 0.5 mM [U-99% 13C; U-99% 15N] BacSp222, 100 mM [U-100% 2H] sodium acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	BacSp222	[U-99% 13C; U-99% 15N]		0.5 mM
2	sodium acetate	[U-100% 2H]		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

6 3D CBCA(CO)NH

Instrument

Varian Uniform NMR System - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 5, Details 0.5 mM [U-99% 13C; U-99% 15N] BacSp222, 100 mM [U-100% 2H] sodium acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	BacSp222	[U-99% 13C; U-99% 15N]		0.5 mM
2	sodium acetate	[U-100% 2H]		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

7 3D 13C-edited NOESY (aromatic

Instrument

Varian Uniform NMR System - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 5, Details 0.5 mM [U-99% 13C; U-99% 15N] BacSp222, 100 mM [U-100% 2H] sodium acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	BacSp222	[U-99% 13C; U-99% 15N]		0.5 mM
2	sodium acetate	[U-100% 2H]		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

8 3D 15N-edited NOESY

Instrument

Varian Uniform NMR System - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 5, Details 0.5 mM [U-99% 13C; U-99% 15N] BacSp222, 100 mM [U-100% 2H] sodium acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	BacSp222	[U-99% 13C; U-99% 15N]		0.5 mM
2	sodium acetate	[U-100% 2H]		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

9 3D HCCH-TOCSY

Instrument

Varian Uniform NMR System - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 5, Details 0.5 mM [U-99% 13C; U-99% 15N] BacSp222, 100 mM [U-100% 2H] sodium acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	BacSp222	[U-99% 13C; U-99% 15N]		0.5 mM
2	sodium acetate	[U-100% 2H]		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

10 3D HBHA(CO)NH

Instrument

Varian Uniform NMR System - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 5, Details 0.5 mM [U-99% 13C; U-99% 15N] BacSp222, 100 mM [U-100% 2H] sodium acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	BacSp222	[U-99% 13C; U-99% 15N]		0.5 mM
2	sodium acetate	[U-100% 2H]		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

11 3D HNCACB

Instrument

Varian Uniform NMR System - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 5, Details 0.5 mM [U-99% 13C; U-99% 15N] BacSp222, 100 mM [U-100% 2H] sodium acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	BacSp222	[U-99% 13C; U-99% 15N]		0.5 mM
2	sodium acetate	[U-100% 2H]		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

12 3D HNCA

Instrument

Varian Uniform NMR System - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 5, Details 0.5 mM [U-99% 13C; U-99% 15N] BacSp222, 100 mM [U-100% 2H] sodium acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	BacSp222	[U-99% 13C; U-99% 15N]		0.5 mM
2	sodium acetate	[U-100% 2H]		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

13 3D HN(CO)CA

Instrument

Varian Uniform NMR System - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 5, Details 0.5 mM [U-99% 13C; U-99% 15N] BacSp222, 100 mM [U-100% 2H] sodium acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	BacSp222	[U-99% 13C; U-99% 15N]		0.5 mM
2	sodium acetate	[U-100% 2H]		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

14 13C-edited NOESY (aliphatic

Instrument

Varian Uniform NMR System - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 5, Details 0.5 mM [U-99% 13C; U-99% 15N] BacSp222, 100 mM [U-100% 2H] sodium acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	BacSp222	[U-99% 13C; U-99% 15N]		0.5 mM
2	sodium acetate	[U-100% 2H]		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34044_5lwc.nef
Input source #2: Coordindates	5lwc.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:1:FME:C	1:2:ALA:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	1	FME	N-FORMYLMETHIONINE	Assigned chemical shifts, Coordinates

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50
XAGLLRFLLSKGRALYNWAKSHVGKVWEWLKSGATYEQIKEWIENALGWR
||||||||||||||||||||||||||||||||||||||||||||||||||
XAGLLRFLLSKGRALYNWAKSHVGKVWEWLKSGATYEQIKEWIENALGWR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	50	0	0	100.0

Content subtype: combined_34044_5lwc.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	589		100.0 (chain: A, length: 50)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	818 (1)	noe	98.0 (chain: A, length: 50)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	85 (85)	.	90.0 (chain: A, length: 50)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 50, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 306
  - ¹³C chemical shifts: 228
  - ¹⁵N chemical shifts: 55
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 50, Sequence coverage: 98.0%
- Total number of restraints: 817
- Weight of restraints: 1.0 (817)
- Potential type of restraints: square-well-parabolic (817)
- Range of distance target values: 1.42, 2.85 (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: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 50, Sequence coverage: 90.0%
- Total number of restraints: 85
- Total number of restraints per polymer type: 85
- Weight of restraints: 1.0 (85)
- Potential type of restraints: square-well-parabolic (85)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Bacteriocin, Structure from MOLMOL