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BMRB: 19882

2MN8

NMR structure of a peptoid analogue of maculatin G15 containing cis-Nleu at position 13

Authors

Uggerhoej, L.E., Guentert, P., Wimmer, R.

Assembly

a peptoid analogue of maculatin G15 containing cis-Nleu at position 13

Entity

1. a peptoid analogue of maculatin G15 containing cis-Nleu at position 13 (polymer, Thiol state: not present), 22 monomers, 2118.500 Da Detail

GLFGVLAKVA AHXVGAIAEH FX

Formula weight

2118.5 Da

Source organism

Ranoidea genimaculata

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 86.4 %, Completeness: 73.5 %, Completeness (bb): 76.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	73.5 % (144 of 196)	88.7 % (94 of 106)	55.6 % (50 of 90)
Backbone	76.0 % (76 of 100)	90.7 % (39 of 43)	64.9 % (37 of 57)
Sidechain	75.2 % (85 of 113)	87.3 % (55 of 63)	60.0 % (30 of 50)
Aromatic	28.6 % (8 of 28)	57.1 % (8 of 14)	0.0 % (0 of 14)
Methyl	76.5 % (26 of 34)	88.2 % (15 of 17)	64.7 % (11 of 17)

1. entity

GLFGVLAKVA AHXVGAIAEH FX

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310.1 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		3 mM
2	sodium azide	natural abundance		2 mM
3	SDS	[U-2H]		150 mM
4	potassium phosphate	natural abundance		10 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2MN8, Strand ID: A Detail

Release date

2014-07-15

Citation

Structural features of peptoid-peptide hybrids in lipid-water interfaces
Uggerhoej, L.E., Munk, J.K., Hansen, P.R., Guentert, P., Wimmer, R.
FEBS Lett. (2014), 588, 3291-3297, PubMed 25063337 , DOI 10.1016/j.febslet.2014.07.016 , Abstract

Related entities 1. a peptoid analogue of maculatin G15 containing cis-Nleu at position 13, : 1 : 3 : 1 entities Detail

Experiments performed 5 experiments Detail

1 2D 1H-1H COSY

Instrument

Bruker Avance - 900 MHz Centre for Biomolecular Magnetic Resonance, Frankfurt, Germany

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310.1 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		3 mM
2	sodium azide	natural abundance		2 mM
3	SDS	[U-2H]		150 mM
4	potassium phosphate	natural abundance		10 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

2 2D 1H-1H TOCSY

Instrument

Bruker Avance - 900 MHz Centre for Biomolecular Magnetic Resonance, Frankfurt, Germany

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310.1 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		3 mM
2	sodium azide	natural abundance		2 mM
3	SDS	[U-2H]		150 mM
4	potassium phosphate	natural abundance		10 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 900 MHz Centre for Biomolecular Magnetic Resonance, Frankfurt, Germany

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310.1 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		3 mM
2	sodium azide	natural abundance		2 mM
3	SDS	[U-2H]		150 mM
4	potassium phosphate	natural abundance		10 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

4 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 900 MHz Centre for Biomolecular Magnetic Resonance, Frankfurt, Germany

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310.1 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		3 mM
2	sodium azide	natural abundance		2 mM
3	SDS	[U-2H]		150 mM
4	potassium phosphate	natural abundance		10 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

5 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 900 MHz Centre for Biomolecular Magnetic Resonance, Frankfurt, Germany

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310.1 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		3 mM
2	sodium azide	natural abundance		2 mM
3	SDS	[U-2H]		150 mM
4	potassium phosphate	natural abundance		10 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19882_2mn8.nef
Input source #2: Coordindates	2mn8.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)
1:12:HIS:C	1:13:I4G:N	unknown	unknown	n/a
1:13:I4G:C	1:14:VAL:N	unknown	unknown	n/a
1:21:PHE:C	1:22:NH2:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	13	I4G	N-(2-methylpropyl)glycine	Assigned chemical shifts, Coordinates
A	22	NH2	AMINO GROUP	Assigned chemical shifts, Coordinates

Sequence alignments

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

--------10--------20--
GLFGVLAKVAAHXVGAIAEHFX
||||||||||||||||||||||
GLFGVLAKVAAHXVGAIAEHFX

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	22	0	0	100.0

Content subtype: combined_19882_2mn8.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	152		95.5 (chain: A, length: 22)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	167 (1)	noe	86.4 (chain: A, length: 22)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	32 (32)	.	90.9 (chain: A, length: 22)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 22, Sequence coverage: 95.5%
- Total number of assignments
  - ¹H chemical shifts: 102
  - ¹³C chemical shifts: 50
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 22, Sequence coverage: 86.4%
- Total number of restraints: 167
- Weight of restraints: 1.0 (167)
- Potential type of restraints: upper-bound-parabolic (167)
- Range of distance target values: 2.4, 5.34 (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: 22, Sequence coverage: 90.9%
- Total number of restraints: 32
- Total number of restraints per polymer type: 32
- Weight of restraints: 1.0 (32)
- Potential type of restraints: square-well-parabolic (32)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords antimicrobial peptide, maculatin, N-substituted glycine, peptoid