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BMRB: 25877

2N92

Solution structure of cecropin P1 with LPS

Authors

Baek, M., Kamiya, M., Kushibiki, T., Nakazumi, T., Tomisawa, S., Abe, C., Kumaki, Y., Kushibiki, T., Kikukawa, T., Demura, M., Kawano, K., Aizawa, T.

Assembly

cecropin P1 with LPS

Entity

1. cecropin P1 with LPS (polymer, Thiol state: not present), 31 monomers, 3338.856 Da Detail

SWLSKTAKKL ENSAKKRISE GIAIAIQGGP R

Formula weight

3338.856 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.8 %, Completeness: 85.8 %, Completeness (bb): 79.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.8 % (313 of 365)	94.3 % (183 of 194)	73.2 % (101 of 138)	87.9 % (29 of 33)
Backbone	79.9 % (147 of 184)	95.3 % (61 of 64)	64.4 % (58 of 90)	93.3 % (28 of 30)
Sidechain	92.3 % (193 of 209)	93.8 % (122 of 130)	92.1 % (70 of 76)	33.3 % (1 of 3)
Aromatic	58.3 % (7 of 12)	100.0 % (6 of 6)	0.0 % (0 of 5)	100.0 % (1 of 1)
Methyl	100.0 % (34 of 34)	100.0 % (17 of 17)	100.0 % (17 of 17)

1. cp1

SWLSKTAKKL ENSAKKRISE GIAIAIQGGP R

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	cp1	natural abundance		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
4	cp1	[U-13C; U-15N]		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
7	cp1	[U-15N]		1 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2N92, Strand ID: A Detail

Release date

2016-06-14

Citation

Lipopolysaccharide-bound structure of the antimicrobial peptide cecropin P1 determined by nuclear magnetic resonance spectroscopy
Baek, M., Kamiya, M., Kushibiki, T., Nakazumi, T., Tomisawa, S., Abe, C., Kumaki, Y., Kushibiki, T., Kikukawa, T., Demura, M., Kawano, K., Aizawa, T.
J. Pept. Sci. (2016), 22, 214-221, PubMed 26939541 , DOI 10.1002/psc.2865 , Abstract

Related entities 1. cecropin P1 with LPS, : 1 : 2 : 1 : 13 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
7	cp1	[U-15N]		1 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
4	cp1	[U-13C; U-15N]		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

3 2D 1H-1H TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	cp1	natural abundance		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

4 2D 1H-1H COSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	cp1	natural abundance		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

5 3D CBCA(CO)NH

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
4	cp1	[U-13C; U-15N]		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

6 3D C(CO)NH

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
4	cp1	[U-13C; U-15N]		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

7 3D HNCA

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
4	cp1	[U-13C; U-15N]		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

8 3D HNCACB

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
4	cp1	[U-13C; U-15N]		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

9 3D HNCACB

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
4	cp1	[U-13C; U-15N]		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

10 3D 1H-15N NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
7	cp1	[U-15N]		1 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

11 3D 1H-15N TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
7	cp1	[U-15N]		1 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

12 3D 1H-13C NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
4	cp1	[U-13C; U-15N]		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25877_2n92.nef
Input source #2: Coordindates	2n92.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	None
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)

None

Non-standard residues

None

Sequence alignments

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

--------10--------20--------30-
SWLSKTAKKLENSAKKRISEGIAIAIQGGPR
|||||||||||||||||||||||||||||||
SWLSKTAKKLENSAKKRISEGIAIAIQGGPR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	31	0	0	100.0

Content subtype: combined_25877_2n92.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	312		96.8 (chain: A, length: 31)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	696 (1)	noe	96.8 (chain: A, length: 31)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 31, Sequence coverage: 96.8%
- Total number of assignments
  - ¹H chemical shifts: 183
  - ¹³C chemical shifts: 100
  - ¹⁵N chemical shifts: 29
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 31, Sequence coverage: 96.8%
- Total number of restraints: 672
- Weight of restraints: 1.0 (672)
- Potential type of restraints: upper-bound-parabolic (672)
- Range of distance target values: 2.4, 7.5 (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

Keywords antimicrobial peptide, lipopolysaccharide