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BMRB: 19856

2MMJ

Structure of a peptoid analogue of maculatin G15 in DPC micelles

Authors

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

Assembly

a peptoid analogue of maculatin G15 in DPC micelles

Entity

1. a peptoid analogue of maculatin G15 in DPC micelles, entity 1 (polymer, Thiol state: not present), 22 monomers, 2146.553 Da Detail

GLFGVLAKVA XHVVGAIAEH FX

2. UNKNOWN ATOM OR ION (non-polymer), na Da

Formula weight

2146.553 Da

Source organism

Ranoidea genimaculata

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 90.9 %, Completeness: 84.0 %, Completeness (bb): 76.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	84.0 % (168 of 200)	95.4 % (103 of 108)	70.7 % (65 of 92)
Backbone	76.0 % (76 of 100)	93.0 % (40 of 43)	63.2 % (36 of 57)
Sidechain	93.2 % (109 of 117)	96.9 % (63 of 65)	88.5 % (46 of 52)
Aromatic	71.4 % (20 of 28)	85.7 % (12 of 14)	57.1 % (8 of 14)
Methyl	100.0 % (36 of 36)	100.0 % (18 of 18)	100.0 % (18 of 18)

1. entity 1

GLFGVLAKVA XHVVGAIAEH FX

Show sample condition

Sample #1

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	DPC	[U-2H]		150 mM
4	potassium phosphate	natural abundance		10 mM
5	H2O	natural abundance		95 %
6	D2O	[U-100% 2H]		5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310.1 K, pH 6.5, Details sample_1 titrated with 2, 5 and 10mM of Gd(DTPA-BMA)

#	Name	Isotope labeling	Type	Concentration
7	entity_1	natural abundance		3 mM
8	sodium azide	natural abundance		2 mM
9	DPC	[U-2H]		150 mM
10	potassium phosphate	natural abundance		10 mM
11	Gd(DTPA-BMA)	natural abundance		2.0 ~ 10.0 mM
12	H2O	natural abundance		95 %
13	D2O	[U-100% 2H]		5 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2MMJ, 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 in DPC micelles, entity 1, : 1 : 4 entities Detail

Experiments performed 6 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	DPC	[U-2H]		150 mM
4	potassium phosphate	natural abundance		10 mM
5	H2O	natural abundance		95 %
6	D2O	[U-100% 2H]		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	DPC	[U-2H]		150 mM
4	potassium phosphate	natural abundance		10 mM
5	H2O	natural abundance		95 %
6	D2O	[U-100% 2H]		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	DPC	[U-2H]		150 mM
4	potassium phosphate	natural abundance		10 mM
5	H2O	natural abundance		95 %
6	D2O	[U-100% 2H]		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	DPC	[U-2H]		150 mM
4	potassium phosphate	natural abundance		10 mM
5	H2O	natural abundance		95 %
6	D2O	[U-100% 2H]		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	DPC	[U-2H]		150 mM
4	potassium phosphate	natural abundance		10 mM
5	H2O	natural abundance		95 %
6	D2O	[U-100% 2H]		5 %

6 pseudo-3D-inversion recovery weighted NOESY

Instrument

Bruker DRX - 600 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, Details sample_1 titrated with 2, 5 and 10mM of Gd(DTPA-BMA)

#	Name	Isotope labeling	Type	Concentration
7	entity_1	natural abundance		3 mM
8	sodium azide	natural abundance		2 mM
9	DPC	[U-2H]		150 mM
10	potassium phosphate	natural abundance		10 mM
11	Gd(DTPA-BMA)	natural abundance		2.0 ~ 10.0 mM
12	H2O	natural abundance		95 %
13	D2O	[U-100% 2H]		5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19856_2mmj.nef
Input source #2: Coordindates	2mmj.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)
1:10:ALA:C	1:11:I4G:N	unknown	unknown	n/a
1:11:I4G:C	1:12:HIS: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	11	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--
GLFGVLAKVAXHVVGAIAEHFX
||||||||||||||||||||||
GLFGVLAKVAXHVVGAIAEHFX

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_19856_2mmj.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	180		100.0 (chain: A, length: 22)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	278 (1)	noe	86.4 (chain: A, length: 22)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	31 (31)	.	86.4 (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: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 112
  - ¹³C chemical shifts: 68
- 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: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 22, Sequence coverage: 86.4%
- Total number of restraints: 275
- Weight of restraints: 1.0 (275)
- Potential type of restraints: square-well-parabolic (275)
- Range of distance target values: 1.76, 4.75 (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: 22, Sequence coverage: 86.4%
- Total number of restraints: 31
- Total number of restraints per polymer type: 31
- Weight of restraints: 1.0 (31)
- Potential type of restraints: square-well-parabolic (31)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

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