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BMRB: 36167

5ZCN

Solution NMR structure of a new lasso peptide brevunsin

Authors

Hemmi, H., Kodani, S., Miyake, Y., Kaweewan, I., Nakagawa, H.

Assembly

brevunsin

Entity

1. brevunsin (polymer, Thiol state: not present), 21 monomers, 2252.456 Da Detail

DGMGEEFIEG LVRDSLYPPA G

Formula weight

2252.456 Da

Source organism

Brevundimonas diminuta

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 79.8 %, Completeness (bb): 72.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	79.8 % (166 of 208)	94.1 % (111 of 118)	61.1 % (55 of 90)
Backbone	72.8 % (75 of 103)	95.5 % (42 of 44)	55.9 % (33 of 59)
Sidechain	84.4 % (103 of 122)	93.2 % (69 of 74)	70.8 % (34 of 48)
Aromatic	100.0 % (18 of 18)	100.0 % (9 of 9)	100.0 % (9 of 9)
Methyl	94.4 % (17 of 18)	100.0 % (9 of 9)	88.9 % (8 of 9)

1. entity 1

DGMGEEFIEG LVRDSLYPPA G

Show sample condition

Sample

Solvent system DMSO, Pressure 1 atm, Temperature 298 K, Details 6 mg/mL brevunsin, DMSO

#	Name	Isotope labeling	Type	Concentration
1	brevunsin	natural abundance	protein	6 mg/mL
2	DMSO-d6	[U-2H]	solvent	100 %

Release date

2018-06-10

Citation

Heterologous production of a new lasso peptide brevunsin in Sphingomonas subterranea
Kodani, S., Hemmi, H., Miyake, Y., Kaweewan, I., Nakagawa, H.
J. Ind. Microbiol. Biotechnol. (2018), 45, 983-992, PubMed 30191430 , DOI 10.1007/s10295-018-2077-6 , Abstract

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system DMSO, Pressure 1 atm, Temperature 298 K, Details 6 mg/mL brevunsin, DMSO

#	Name	Isotope labeling	Type	Concentration
1	brevunsin	natural abundance	protein	6 mg/mL
2	DMSO-d6	[U-2H]	solvent	100 %

2 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system DMSO, Pressure 1 atm, Temperature 298 K, Details 6 mg/mL brevunsin, DMSO

#	Name	Isotope labeling	Type	Concentration
1	brevunsin	natural abundance	protein	6 mg/mL
2	DMSO-d6	[U-2H]	solvent	100 %

3 2D 1H-13C HMBC

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system DMSO, Pressure 1 atm, Temperature 298 K, Details 6 mg/mL brevunsin, DMSO

#	Name	Isotope labeling	Type	Concentration
1	brevunsin	natural abundance	protein	6 mg/mL
2	DMSO-d6	[U-2H]	solvent	100 %

4 2D 1H-1H TOCSY

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system DMSO, Pressure 1 atm, Temperature 298 K, Details 6 mg/mL brevunsin, DMSO

#	Name	Isotope labeling	Type	Concentration
1	brevunsin	natural abundance	protein	6 mg/mL
2	DMSO-d6	[U-2H]	solvent	100 %

5 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system DMSO, Pressure 1 atm, Temperature 298 K, Details 6 mg/mL brevunsin, DMSO

#	Name	Isotope labeling	Type	Concentration
1	brevunsin	natural abundance	protein	6 mg/mL
2	DMSO-d6	[U-2H]	solvent	100 %

6 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system DMSO, Pressure 1 atm, Temperature 298 K, Details 6 mg/mL brevunsin, DMSO

#	Name	Isotope labeling	Type	Concentration
1	brevunsin	natural abundance	protein	6 mg/mL
2	DMSO-d6	[U-2H]	solvent	100 %

7 2D 1H-1H NOESY

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system DMSO, Pressure 1 atm, Temperature 298 K, Details 6 mg/mL brevunsin, DMSO

#	Name	Isotope labeling	Type	Concentration
1	brevunsin	natural abundance	protein	6 mg/mL
2	DMSO-d6	[U-2H]	solvent	100 %

8 2D DQF-COSY

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system DMSO, Pressure 1 atm, Temperature 298 K, Details 6 mg/mL brevunsin, DMSO

#	Name	Isotope labeling	Type	Concentration
1	brevunsin	natural abundance	protein	6 mg/mL
2	DMSO-d6	[U-2H]	solvent	100 %

9 1D 1H

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system DMSO, Pressure 1 atm, Temperature 298 K, Details 6 mg/mL brevunsin, DMSO

#	Name	Isotope labeling	Type	Concentration
1	brevunsin	natural abundance	protein	6 mg/mL
2	DMSO-d6	[U-2H]	solvent	100 %

10 1D 13C

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system DMSO, Pressure 1 atm, Temperature 298 K, Details 6 mg/mL brevunsin, DMSO

#	Name	Isotope labeling	Type	Concentration
1	brevunsin	natural abundance	protein	6 mg/mL
2	DMSO-d6	[U-2H]	solvent	100 %

11 DEPT135

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system DMSO, Pressure 1 atm, Temperature 298 K, Details 6 mg/mL brevunsin, DMSO

#	Name	Isotope labeling	Type	Concentration
1	brevunsin	natural abundance	protein	6 mg/mL
2	DMSO-d6	[U-2H]	solvent	100 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_36167_5zcn.nef
Input source #2: Coordindates	5zcn.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:ASP:N	1:9:GLU:CD	unknown	unknown	n/a

Non-standard residues

None

Sequence alignments

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

--------10--------20-
DGMGEEFIEGLVRDSLYPPAG
|||||||||||||||||||||
DGMGEEFIEGLVRDSLYPPAG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	21	0	0	100.0

Content subtype: combined_36167_5zcn.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	161		100.0 (chain: A, length: 21)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	242 (1)	noe	100.0 (chain: A, length: 21)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	5 (5)	.	42.9 (chain: A, length: 21)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 112
  - ¹³C chemical shifts: 49
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 100.0%
- Total number of restraints: 241
- Weight of restraints: 1.0 (241)
- Potential type of restraints: square-well-parabolic (241)
- Range of distance target values: 2.35, 5.8 (Å)
- Histogram of 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: 21, Sequence coverage: 42.9%
- Total number of restraints: 5
- Total number of restraints per polymer type: 5
- Weight of restraints: 1.0 (5)
- Potential type of restraints: square-well-parabolic (5)
- Dihedral angle restraints per residue

Keywords Sphingomonas subterranea, UNKNOWN FUNCTION, brevunsin, lasso peptide