BMRBj - BMREntryMaster

	Total	¹H	¹³C	¹⁵N
All	87.1 % (278 of 319)	94.6 % (158 of 167)	75.8 % (94 of 124)	92.9 % (26 of 28)
Backbone	81.2 % (125 of 154)	96.3 % (52 of 54)	66.7 % (50 of 75)	92.0 % (23 of 25)
Sidechain	93.6 % (176 of 188)	93.8 % (106 of 113)	93.1 % (67 of 72)	100.0 % (3 of 3)
Aromatic	16.7 % (2 of 12)	16.7 % (1 of 6)	0.0 % (0 of 5)	100.0 % (1 of 1)
Methyl	100.0 % (44 of 44)	100.0 % (22 of 22)	100.0 % (22 of 22)

1. Melittin

GIGAVLKVLT TGLPALISWI KRKRQQ

Show sample condition

Sample #1

Solvent system trifluoroethanol/water, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.05 mM [U-95% 13C; U-95% 15N] melittin, 10% w/v deuterated glycerol (to increase viscosity), 30% v/v deuterated trifluoroethanol (to stabilize helical structure), and 10% v/v deuterium oxide in 10 mM potassium phosphate buffer at pH 7

#	Name	Isotope labeling	Concentration
1	melittin	[U-95% 13C; U-95% 15N]	0.05 mM
2	glycerol	[U-2H]	10 % v/v
3	potassium phosphate buffer	natural abundance	10 mM

Sample #2

Solvent system trifluoroethanol/water, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.050 mM [U-95% 13C; U-95% 15N] Melittin, 30% v/v deuterated trifluoroethanol (to stabilize helical structure), and 10% v/v deuterium oxide in 10 mM potassium phosphate buffer at pH 7

#	Name	Isotope labeling	Type	Concentration
4	Melittin	[U-95% 13C; U-95% 15N]		0.050 mM
5	potassium phosphate buffer	natural abundance		10 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 6DST, Strand ID: A Detail

Release date

2018-07-05

Citation

Nuclear Magnetic Resonance-Based Structural Characterization and Backbone Dynamics of Recombinant Bee Venom Melittin
Ramirez, L.M., Pande, J., Shekhtman, A., Ramirez, L., Shekhtman, A., Pande, J.
Biochemistry (2018), 57, 2775-2785, PubMed 29668274 , DOI 10.1021/acs.biochem.8b00156 , Abstract

Related entities 1. Melittin, : 1 : 10 : 2 : 1 : 15 entities Detail

Experiments performed 9 experiments Detail

1 3D 1H-15N NOESY

Instrument

Bruker AvanceII - 700 MHz

Sample

State isotropic, Solvent system trifluoroethanol/water, Pressure 1 atm, Temperature 285 K, pH 7, Details 0.05 mM [U-95% 13C; U-95% 15N] melittin, 10% w/v deuterated glycerol (to increase viscosity), 30% v/v deuterated trifluoroethanol (to stabilize helical structure), and 10% v/v deuterium oxide in 10 mM potassium phosphate buffer at pH 7

#	Name	Isotope labeling	Concentration
1	melittin	[U-95% 13C; U-95% 15N]	0.05 mM
2	glycerol	[U-2H]	10 % v/v
3	potassium phosphate buffer	natural abundance	10 mM

2 3D 1H-13C NOESY

Instrument

Bruker AvanceII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	melittin	[U-95% 13C; U-95% 15N]	0.05 mM
2	glycerol	[U-2H]	10 % v/v
3	potassium phosphate buffer	natural abundance	10 mM

3 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system trifluoroethanol/water, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.05 mM [U-95% 13C; U-95% 15N] melittin, 10% w/v deuterated glycerol (to increase viscosity), 30% v/v deuterated trifluoroethanol (to stabilize helical structure), and 10% v/v deuterium oxide in 10 mM potassium phosphate buffer at pH 7

#	Name	Isotope labeling	Concentration
1	melittin	[U-95% 13C; U-95% 15N]	0.05 mM
2	glycerol	[U-2H]	10 % v/v
3	potassium phosphate buffer	natural abundance	10 mM

4 3D HNCA

Instrument

Bruker AvanceII - 700 MHz

Sample

State isotropic, Solvent system trifluoroethanol/water, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.050 mM [U-95% 13C; U-95% 15N] Melittin, 30% v/v deuterated trifluoroethanol (to stabilize helical structure), and 10% v/v deuterium oxide in 10 mM potassium phosphate buffer at pH 7

#	Name	Isotope labeling	Type	Concentration
4	Melittin	[U-95% 13C; U-95% 15N]		0.050 mM
5	potassium phosphate buffer	natural abundance		10 mM

5 3D HNCACB

Instrument

Bruker AvanceII - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
4	Melittin	[U-95% 13C; U-95% 15N]		0.050 mM
5	potassium phosphate buffer	natural abundance		10 mM

6 2D 1H-15N HSQC

Instrument

Bruker AvanceII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	melittin	[U-95% 13C; U-95% 15N]	0.05 mM
2	glycerol	[U-2H]	10 % v/v
3	potassium phosphate buffer	natural abundance	10 mM

7 2D 1H-15N HSQC

Instrument

Bruker AvanceII - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
4	Melittin	[U-95% 13C; U-95% 15N]		0.050 mM
5	potassium phosphate buffer	natural abundance		10 mM

8 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	melittin	[U-95% 13C; U-95% 15N]	0.05 mM
2	glycerol	[U-2H]	10 % v/v
3	potassium phosphate buffer	natural abundance	10 mM

9 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceII - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
4	Melittin	[U-95% 13C; U-95% 15N]		0.050 mM
5	potassium phosphate buffer	natural abundance		10 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30481_6dst.nef
Input source #2: Coordindates	6dst.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------
GIGAVLKVLTTGLPALISWIKRKRQQ
||||||||||||||||||||||||||
GIGAVLKVLTTGLPALISWIKRKRQQ

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	26	0	0	100.0

Content subtype: combined_30481_6dst.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	277		100.0 (chain: A, length: 26)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	423 (1)	noe	96.2 (chain: A, length: 26)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	30 (1)	noe	15.4 (chain: A, length: 26)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	249 (249)	.	100.0 (chain: A, length: 26)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 26, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 158
  - ¹³C chemical shifts: 93
  - ¹⁵N chemical shifts: 26
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	167	158	94.6
¹³C chemical shifts	124	93	75.0
¹⁵N chemical shifts	30	26	86.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	52	96.3
¹³C chemical shifts	52	26	50.0
¹⁵N chemical shifts	25	23	92.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	113	106	93.8
¹³C chemical shifts	72	67	93.1
¹⁵N chemical shifts	5	3	60.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	22	22	100.0
¹³C chemical shifts	22	22	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	1	16.7
¹³C chemical shifts	5	0	0.0
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 26, Sequence coverage: 96.2%
- Total number of restraints: 423
- Weight of restraints: 1.0 (423)
- Potential type of restraints: upper-bound-parabolic (423)
- Range of distance target values: 2.4, 5.5 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_4
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 26, Sequence coverage: 15.4%
  - Total number of restraints: 30
  - Weight of restraints: 1.0 (30)
  - Potential type of restraints: upper-bound-parabolic (30)
  - Range of distance target values: 5.0, 5.0 (Å)
  - 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: 26, Sequence coverage: 100.0%
- Total number of restraints: 249
- Total number of restraints per polymer type: 249
- Weight of restraints: 1.0 (249)
- Potential type of restraints: square-well-parabolic (249)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Alpha-helical peptide, Antibacterial, Bee venom, Hemolytic, TOXIN

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Found 1 Document (0.567 seconds)

BMRB: 30481

Sample #1

Sample #2

Related entities 1. Melittin, : 1 : 10 : 2 : 1 : 15 entities Detail

Experiments performed 9 experiments Detail

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NMR combined restraints 5 contents Detail