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BMRB: 15021

2I7U

Structural and Dynamical Analysis of a Four-Alpha-Helix Bundle with Designed Anesthetic Binding Pockets

Authors

Ma, D., Brandon, N., Cui, T., Bondarenko, V., Canlas, C., Johansson, J., Tang, P., Xu, Y.

Assembly

homodimer

Entity

1. homodimer (polymer, Thiol state: all free), 62 monomers, 6862.980 Da Detail

MKKLREEAAK LFEEWKKLAE EAAKLLEGGG GGGGGELMKL CEEAAKKAEE LFKLAEERLK KL

Formula weight

6862.98 Da

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 85.9 %, Completeness (bb): 97.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.9 % (638 of 743)	91.2 % (361 of 396)	76.1 % (216 of 284)	96.8 % (61 of 63)
Backbone	97.8 % (364 of 372)	98.5 % (130 of 132)	97.2 % (173 of 178)	98.4 % (61 of 62)
Sidechain	77.2 % (328 of 425)	87.5 % (231 of 264)	60.6 % (97 of 160)	0.0 % (0 of 1)
Aromatic	18.8 % (6 of 32)	37.5 % (6 of 16)	0.0 % (0 of 15)	0.0 % (0 of 1)
Methyl	74.2 % (46 of 62)	100.0 % (31 of 31)	48.4 % (15 of 31)

1. Four-alpha-helix bundle

MKKLREEAAK LFEEWKKLAE EAAKLLEGGG GGGGGELMKL CEEAAKKAEE LFKLAEERLK KL

Show sample condition

Sample

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.5, Details 0.5mM 4HB U-15N,13C, 90% H2O, 10% D2O, 0.2mM DSS

#	Name	Isotope labeling	Type	Concentration
1	Four-alpha-helix bundle	[U-100% 13C; U-100% 15N]		0.5 mM
2	DSS			0.2 mM
3	H2O			90 %
4	D2O			10 %

Protein Blocks Logo

Calculated from 10 models in PDB: 2I7U, Strand ID: A, B Detail

Release date

2008-06-23

Citation

Four-alpha-helix bundle with designed anesthetic binding pockets. Part I: structural and dynamical analyses
Ma, D., Brandon, N.R., Cui, T., Bondarenko, V., Canlas, C., Johansson, J.S., Tang, P., Xu, Y.
Biophys. J. (2008), 94, 4454-4463, PubMed 18310240 , DOI 10.1529/biophysj.107.117838 , Abstract

Related entities 1. homodimer, : 1 : 1 : 6 entities Detail

Experiments performed 14 experiments Detail

1 3D_15N-separated_NOESY

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.5, Details 0.5mM 4HB U-15N,13C, 90% H2O, 10% D2O, 0.2mM DSS

#	Name	Isotope labeling	Type	Concentration
1	Four-alpha-helix bundle	[U-100% 13C; U-100% 15N]		0.5 mM
2	DSS			0.2 mM
3	H2O			90 %
4	D2O			10 %

2 3D_13C-separated_NOESY

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.5, Details 0.5mM 4HB U-15N,13C, 90% H2O, 10% D2O, 0.2mM DSS

#	Name	Isotope labeling	Type	Concentration
1	Four-alpha-helix bundle	[U-100% 13C; U-100% 15N]		0.5 mM
2	DSS			0.2 mM
3	H2O			90 %
4	D2O			10 %

3 HNCO

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.5, Details 0.5mM 4HB U-15N,13C, 90% H2O, 10% D2O, 0.2mM DSS

#	Name	Isotope labeling	Type	Concentration
1	Four-alpha-helix bundle	[U-100% 13C; U-100% 15N]		0.5 mM
2	DSS			0.2 mM
3	H2O			90 %
4	D2O			10 %

4 CBCACONH

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.5, Details 0.5mM 4HB U-15N,13C, 90% H2O, 10% D2O, 0.2mM DSS

#	Name	Isotope labeling	Type	Concentration
1	Four-alpha-helix bundle	[U-100% 13C; U-100% 15N]		0.5 mM
2	DSS			0.2 mM
3	H2O			90 %
4	D2O			10 %

5 HNCACB

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.5, Details 0.5mM 4HB U-15N,13C, 90% H2O, 10% D2O, 0.2mM DSS

#	Name	Isotope labeling	Type	Concentration
1	Four-alpha-helix bundle	[U-100% 13C; U-100% 15N]		0.5 mM
2	DSS			0.2 mM
3	H2O			90 %
4	D2O			10 %

6 2D NOESY

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.5, Details 0.5mM 4HB U-15N,13C, 90% H2O, 10% D2O, 0.2mM DSS

#	Name	Isotope labeling	Type	Concentration
1	Four-alpha-helix bundle	[U-100% 13C; U-100% 15N]		0.5 mM
2	DSS			0.2 mM
3	H2O			90 %
4	D2O			10 %

7 HSQC

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.5, Details 0.5mM 4HB U-15N,13C, 90% H2O, 10% D2O, 0.2mM DSS

#	Name	Isotope labeling	Type	Concentration
1	Four-alpha-helix bundle	[U-100% 13C; U-100% 15N]		0.5 mM
2	DSS			0.2 mM
3	H2O			90 %
4	D2O			10 %

8 HNCA

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.5, Details 0.5mM 4HB U-15N,13C, 90% H2O, 10% D2O, 0.2mM DSS

#	Name	Isotope labeling	Type	Concentration
1	Four-alpha-helix bundle	[U-100% 13C; U-100% 15N]		0.5 mM
2	DSS			0.2 mM
3	H2O			90 %
4	D2O			10 %

9 HNCOCA

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.5, Details 0.5mM 4HB U-15N,13C, 90% H2O, 10% D2O, 0.2mM DSS

#	Name	Isotope labeling	Type	Concentration
1	Four-alpha-helix bundle	[U-100% 13C; U-100% 15N]		0.5 mM
2	DSS			0.2 mM
3	H2O			90 %
4	D2O			10 %

10 HBHA(CO)NH

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.5, Details 0.5mM 4HB U-15N,13C, 90% H2O, 10% D2O, 0.2mM DSS

#	Name	Isotope labeling	Type	Concentration
1	Four-alpha-helix bundle	[U-100% 13C; U-100% 15N]		0.5 mM
2	DSS			0.2 mM
3	H2O			90 %
4	D2O			10 %

11 HBHANH

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.5, Details 0.5mM 4HB U-15N,13C, 90% H2O, 10% D2O, 0.2mM DSS

#	Name	Isotope labeling	Type	Concentration
1	Four-alpha-helix bundle	[U-100% 13C; U-100% 15N]		0.5 mM
2	DSS			0.2 mM
3	H2O			90 %
4	D2O			10 %

12 R1 Relaxation

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.5, Details 0.5mM 4HB U-15N,13C, 90% H2O, 10% D2O, 0.2mM DSS

#	Name	Isotope labeling	Type	Concentration
1	Four-alpha-helix bundle	[U-100% 13C; U-100% 15N]		0.5 mM
2	DSS			0.2 mM
3	H2O			90 %
4	D2O			10 %

13 R2 Relaxation

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.5, Details 0.5mM 4HB U-15N,13C, 90% H2O, 10% D2O, 0.2mM DSS

#	Name	Isotope labeling	Type	Concentration
1	Four-alpha-helix bundle	[U-100% 13C; U-100% 15N]		0.5 mM
2	DSS			0.2 mM
3	H2O			90 %
4	D2O			10 %

14 Heteronuclear NOE

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 4.5, Details 0.5mM 4HB U-15N,13C, 90% H2O, 10% D2O, 0.2mM DSS

#	Name	Isotope labeling	Type	Concentration
1	Four-alpha-helix bundle	[U-100% 13C; U-100% 15N]		0.5 mM
2	DSS			0.2 mM
3	H2O			90 %
4	D2O			10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15021_2i7u.nef
Input source #2: Coordindates	2i7u.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--------40--------50--------60--
MKKLREEAAKLFEEWKKLAEEAAKLLEGGGGGGGGELMKLCEEAAKKAEELFKLAEERLKKL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKKLREEAAKLFEEWKKLAEEAAKLLEGGGGGGGGELMKLCEEAAKKAEELFKLAEERLKKL

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

--------10--------20--------30--------40--------50--------60--
MKKLREEAAKLFEEWKKLAEEAAKLLEGGGGGGGGELMKLCEEAAKKAEELFKLAEERLKKL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKKLREEAAKLFEEWKKLAEEAAKLLEGGGGGGGGELMKLCEEAAKKAEELFKLAEERLKKL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	62	0	0	100.0
B	B	62	0	0	100.0

Content subtype: combined_15021_2i7u.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	627		100.0 (chain: A, length: 62)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1498 (1)	noe	96.8 (chain: A, length: 62), 96.8 (chain: B, length: 62)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	80 (1)	hbond	45.2 (chain: A, length: 62), 45.2 (chain: B, length: 62)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	180 (180)	.	79.0 (chain: A, length: 62), 79.0 (chain: B, length: 62)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 62, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 360
  - ¹³C chemical shifts: 206
  - ¹⁵N chemical shifts: 61
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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: 62, Sequence coverage: 96.8%
  - Entity_assembly_ID: B, Chain length: 62, Sequence coverage: 96.8%
- Total number of restraints: 1463
- Weight of restraints: 1.0 (1463)
- Potential type of restraints: upper-bound-parabolic (1463)
- Range of distance target values: 2.51, 6.19 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_4
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 62, Sequence coverage: 45.2%
    - Entity_assembly_ID: B, Chain length: 62, Sequence coverage: 45.2%
  - Total number of restraints: 80
  - Weight of restraints: 1.0 (80)
  - Potential type of restraints: upper-bound-parabolic (80)
  - Range of distance target values: 1.79, 2.68 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - 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: 62, Sequence coverage: 79.0%
  - Entity_assembly_ID: B, Chain length: 62, Sequence coverage: 79.0%
- Total number of restraints: 180
- Total number of restraints per polymer type: 180
- Weight of restraints: 1.0 (180)
- Potential type of restraints: square-well-parabolic (180)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords ALPHA HELIX, ANESTHETIC BINDING, FOUR-ALPHA-HELIX BUNDLE, HOMO DIMER