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BMRB: 18861

2M1F

NMR Structure of Antiamoebin I (peptaibol antibiotic) bound to DMPC/DHPC bicelles

Authors

Shenkarev, Z.O., Paramonov, A.S., Gizatullina, A.K.

Assembly

Antiamoebin I

Entity

1. Antiamoebin I (polymer, Thiol state: not present), 17 monomers, 1654.990 Da Detail

XFXXXXGLXX XQXXXPX

Formula weight

1654.99 Da

Source organism

Emericellopsis minima

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 29.4 %, Completeness: 84.4 %, Completeness (bb): 100.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.4 % (54 of 64)	85.3 % (29 of 34)	80.0 % (20 of 25)	100.0 % (5 of 5)
Backbone	100.0 % (28 of 28)	100.0 % (10 of 10)	100.0 % (14 of 14)	100.0 % (4 of 4)
Sidechain	75.0 % (30 of 40)	79.2 % (19 of 24)	66.7 % (10 of 15)	100.0 % (1 of 1)
Aromatic	0.0 % (0 of 10)	0.0 % (0 of 5)	0.0 % (0 of 5)
Methyl	100.0 % (4 of 4)	100.0 % (2 of 2)	100.0 % (2 of 2)

1. ANTIAMOEBIN I

XFXXXXGLXX XQXXXPX

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.1

#	Name	Isotope labeling	Type	Concentration
1	DHPC	natural abundance		120 mM
2	DMPC	natural abundance		30 mM
3	acetic acid	natural abundance		7.5 mM
4	sodium acetate	natural abundance		2.5 mM
5	ANTIAMOEBIN I	[U-100% 13C; U-100% 15N]		1 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2M1F, Strand ID: A Detail

Release date

2012-12-03

Citation

Peptaibol antiamoebin I: spatial structure, backbone dynamics, interaction with bicelles and lipid-protein nanodiscs, and pore formation in context of barrel-stave model
Shenkarev, Z.O., Paramonov, A.S., Lyukmanova, E.N., Gizatullina, A.K., Zhuravleva, A.V., Tagaev, A.A., Yakimenko, Z.A., Telezhinskaya, I.N., Kirpichnikov, M.P., Ovchinnikova, T.V., Arseniev, A.S.
Chem. Biodivers. (2013), 10, 838-863, PubMed 23681729 , DOI 10.1002/cbdv.201200421 , Abstract

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.1

#	Name	Isotope labeling	Type	Concentration
1	DHPC	natural abundance		120 mM
2	DMPC	natural abundance		30 mM
3	acetic acid	natural abundance		7.5 mM
4	sodium acetate	natural abundance		2.5 mM
5	ANTIAMOEBIN I	[U-100% 13C; U-100% 15N]		1 mM

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.1

#	Name	Isotope labeling	Type	Concentration
1	DHPC	natural abundance		120 mM
2	DMPC	natural abundance		30 mM
3	acetic acid	natural abundance		7.5 mM
4	sodium acetate	natural abundance		2.5 mM
5	ANTIAMOEBIN I	[U-100% 13C; U-100% 15N]		1 mM

3 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.1

#	Name	Isotope labeling	Type	Concentration
1	DHPC	natural abundance		120 mM
2	DMPC	natural abundance		30 mM
3	acetic acid	natural abundance		7.5 mM
4	sodium acetate	natural abundance		2.5 mM
5	ANTIAMOEBIN I	[U-100% 13C; U-100% 15N]		1 mM

4 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.1

#	Name	Isotope labeling	Type	Concentration
1	DHPC	natural abundance		120 mM
2	DMPC	natural abundance		30 mM
3	acetic acid	natural abundance		7.5 mM
4	sodium acetate	natural abundance		2.5 mM
5	ANTIAMOEBIN I	[U-100% 13C; U-100% 15N]		1 mM

5 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.1

#	Name	Isotope labeling	Type	Concentration
1	DHPC	natural abundance		120 mM
2	DMPC	natural abundance		30 mM
3	acetic acid	natural abundance		7.5 mM
4	sodium acetate	natural abundance		2.5 mM
5	ANTIAMOEBIN I	[U-100% 13C; U-100% 15N]		1 mM

6 3D HNHA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.1

#	Name	Isotope labeling	Type	Concentration
1	DHPC	natural abundance		120 mM
2	DMPC	natural abundance		30 mM
3	acetic acid	natural abundance		7.5 mM
4	sodium acetate	natural abundance		2.5 mM
5	ANTIAMOEBIN I	[U-100% 13C; U-100% 15N]		1 mM

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.1

#	Name	Isotope labeling	Type	Concentration
1	DHPC	natural abundance		120 mM
2	DMPC	natural abundance		30 mM
3	acetic acid	natural abundance		7.5 mM
4	sodium acetate	natural abundance		2.5 mM
5	ANTIAMOEBIN I	[U-100% 13C; U-100% 15N]		1 mM

8 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.1

#	Name	Isotope labeling	Type	Concentration
1	DHPC	natural abundance		120 mM
2	DMPC	natural abundance		30 mM
3	acetic acid	natural abundance		7.5 mM
4	sodium acetate	natural abundance		2.5 mM
5	ANTIAMOEBIN I	[U-100% 13C; U-100% 15N]		1 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18861_2m1f.nef
Input source #2: Coordindates	2m1f.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:ACE:C	1:2:PHE:N	unknown	unknown	n/a
1:2:PHE:C	1:3:AIB:N	unknown	unknown	n/a
1:3:AIB:C	1:4:AIB:N	unknown	unknown	n/a
1:4:AIB:C	1:5:AIB:N	unknown	unknown	n/a
1:5:AIB:C	1:6:DIV:N	unknown	unknown	n/a
1:6:DIV:C	1:7:GLY:N	unknown	unknown	n/a
1:8:LEU:C	1:9:AIB:N	unknown	unknown	n/a
1:9:AIB:C	1:10:AIB:N	unknown	unknown	n/a
1:10:AIB:C	1:11:HYP:N	unknown	unknown	n/a
1:11:HYP:C	1:12:GLN:N	unknown	unknown	n/a
1:12:GLN:C	1:13:DIV:N	unknown	unknown	n/a
1:13:DIV:C	1:14:HYP:N	unknown	unknown	n/a
1:14:HYP:C	1:15:AIB:N	unknown	unknown	n/a
1:15:AIB:C	1:16:PRO:N	unknown	unknown	n/a
1:16:PRO:C	1:17:PHL:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	1	ACE	ACETYL GROUP	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	3	AIB	ALPHA-AMINOISOBUTYRIC ACID	Assigned chemical shifts, Distance restraints, Coordinates
A	4	AIB	ALPHA-AMINOISOBUTYRIC ACID	Assigned chemical shifts, Distance restraints, Coordinates
A	5	AIB	ALPHA-AMINOISOBUTYRIC ACID	Assigned chemical shifts, Distance restraints, Coordinates
A	6	DIV	D-ISOVALINE	Assigned chemical shifts, Distance restraints, Coordinates
A	9	AIB	ALPHA-AMINOISOBUTYRIC ACID	Assigned chemical shifts, Distance restraints, Coordinates
A	10	AIB	ALPHA-AMINOISOBUTYRIC ACID	Assigned chemical shifts, Distance restraints, Coordinates
A	11	HYP	4-HYDROXYPROLINE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	13	DIV	D-ISOVALINE	Assigned chemical shifts, Distance restraints, Coordinates
A	14	HYP	4-HYDROXYPROLINE	Assigned chemical shifts, Distance restraints, Coordinates
A	15	AIB	ALPHA-AMINOISOBUTYRIC ACID	Assigned chemical shifts, Distance restraints, Coordinates
A	17	PHL	L-PHENYLALANINOL	Assigned chemical shifts, Distance restraints, Coordinates

Sequence alignments

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

--------10-------
XFXXXXGLXXXQXXXPX
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XFXXXXGLXXXQXXXPX

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	17	0	0	100.0

Content subtype: combined_18861_2m1f.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	15		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	153		100.0 (chain: A, length: 17)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	175 (1)	noe	64.7 (chain: A, length: 17)
2	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	48 (1)	hbond	52.9 (chain: A, length: 17)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	3 (3)	.	35.3 (chain: A, length: 17)
2	Dihedral angle restraints	DYANA/DIANA_dihedral_4	Warning	3 (3)	.	17.6 (chain: A, length: 17)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 75
  - ¹³C chemical shifts: 64
  - ¹⁵N chemical shifts: 14
- 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: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 64.7%
- Total number of restraints: 174
- Weight of restraints: 1.0 (174)
- Potential type of restraints: upper-bound-parabolic (174)
- Range of distance target values: 0.0, 7.0 (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
- Saveframe: DYANA/DIANA_distance_constraints_5
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 52.9%
  - Total number of restraints: 48
  - Weight of restraints: 1.0 (48)
  - Potential type of restraints: upper-bound-parabolic (48)
  - Range of distance target values: 1.8, 3.5 (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: 17, Sequence coverage: 35.3%
- Total number of restraints: 3
- Total number of restraints per polymer type: 3
- Weight of restraints: 1.0 (3)
- Potential type of restraints: square-well-parabolic (3)
- Dihedral angle restraints per residue
- Saveframe: DYANA/DIANA_dihedral_4
  - Status: Warning
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 17.6%
  - Total number of restraints: 3
  - Total number of restraints per polymer type: 3
  - Weight of restraints: 1.0 (3)
  - Potential type of restraints: square-well-parabolic (3)
  - Dihedral angle restraints per residue

Keywords antibiotic, membrane-active, NMR, peptaibol