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BMRB: 15870

2K6I

The domain features of the peripheral stalk subunit H of the methanogenic A1AO ATP synthase and the NMR solution structure of H1-47

Authors

Biukovic, G., Gayen, S., Pervushin, K., Gruber, G.

Assembly

H1-47 subunit A ATP synthase

Entity

1. H1-47 subunit A ATP synthase (polymer, Thiol state: all free), 47 monomers, 5200.005 Da Detail

MGVSVMEAIK EVKLAEEQAV KEIEEAKNRA EQIKAEAIEE AKKLIAC

Formula weight

5200.005 Da

Source organism

Methanocaldococcus jannaschii

Exptl. method

Refine. method

TORSION ANGLE DYNAMICS

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 89.0 %, Completeness (bb): 82.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.0 % (487 of 547)	96.5 % (278 of 288)	76.6 % (160 of 209)	98.0 % (49 of 50)
Backbone	82.6 % (233 of 282)	98.9 % (94 of 95)	66.4 % (93 of 140)	97.9 % (46 of 47)
Sidechain	96.5 % (300 of 311)	95.3 % (184 of 193)	98.3 % (113 of 115)	100.0 % (3 of 3)
Methyl	100.0 % (62 of 62)	100.0 % (31 of 31)	100.0 % (31 of 31)

1. H1-47 subunit A ATP synthase

MGVSVMEAIK EVKLAEEQAV KEIEEAKNRA EQIKAEAIEE AKKLIAC

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	H1-47 subunit A ATP synthase	[U-99% 13C; U-99% 15N]		0.5 - 1 mM
2	sodium azide	natural abundance		0.1 %
3	H2O	natural abundance		90 %
4	D2O	[U-100% 2H]		10 %

Protein Blocks Logo

Calculated from 10 models in PDB: 2K6I, Strand ID: A Detail

Release date

2009-07-09

Citation

Domain features of the peripheral stalk subunit H of the methanogenic A1AO ATP synthase and the NMR solution structure of H(1-47)
Biukovic, G., Gayen, S., Pervushin, K., Gruber, G.
Biophys. J. (2009), 97, 286-294, PubMed 19580766 , DOI 10.1016/j.bpj.2009.04.026 , Abstract

Related entities 1. H1-47 subunit A ATP synthase, : 1 : 2 : 2 entities Detail

Experiments performed 8 experiments Detail

1 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz Bruker Avance 600 MHz equipped with 5 mm triple resonance single axis gradient probe and a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	H1-47 subunit A ATP synthase	[U-99% 13C; U-99% 15N]		0.5 - 1 mM
2	sodium azide	natural abundance		0.1 %
3	H2O	natural abundance		90 %
4	D2O	[U-100% 2H]		10 %

2 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz Bruker Avance 600 MHz equipped with 5 mm triple resonance single axis gradient probe and a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	H1-47 subunit A ATP synthase	[U-99% 13C; U-99% 15N]		0.5 - 1 mM
2	sodium azide	natural abundance		0.1 %
3	H2O	natural abundance		90 %
4	D2O	[U-100% 2H]		10 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz Bruker Avance 600 MHz equipped with 5 mm triple resonance single axis gradient probe and a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	H1-47 subunit A ATP synthase	[U-99% 13C; U-99% 15N]		0.5 - 1 mM
2	sodium azide	natural abundance		0.1 %
3	H2O	natural abundance		90 %
4	D2O	[U-100% 2H]		10 %

4 3D HNCACB

Instrument

Bruker Avance - 600 MHz Bruker Avance 600 MHz equipped with 5 mm triple resonance single axis gradient probe and a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	H1-47 subunit A ATP synthase	[U-99% 13C; U-99% 15N]		0.5 - 1 mM
2	sodium azide	natural abundance		0.1 %
3	H2O	natural abundance		90 %
4	D2O	[U-100% 2H]		10 %

5 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz Bruker Avance 600 MHz equipped with 5 mm triple resonance single axis gradient probe and a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	H1-47 subunit A ATP synthase	[U-99% 13C; U-99% 15N]		0.5 - 1 mM
2	sodium azide	natural abundance		0.1 %
3	H2O	natural abundance		90 %
4	D2O	[U-100% 2H]		10 %

6 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz Bruker Avance 600 MHz equipped with 5 mm triple resonance single axis gradient probe and a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	H1-47 subunit A ATP synthase	[U-99% 13C; U-99% 15N]		0.5 - 1 mM
2	sodium azide	natural abundance		0.1 %
3	H2O	natural abundance		90 %
4	D2O	[U-100% 2H]		10 %

7 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz Bruker Avance 600 MHz equipped with 5 mm triple resonance single axis gradient probe and a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	H1-47 subunit A ATP synthase	[U-99% 13C; U-99% 15N]		0.5 - 1 mM
2	sodium azide	natural abundance		0.1 %
3	H2O	natural abundance		90 %
4	D2O	[U-100% 2H]		10 %

8 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz Bruker Avance 600 MHz equipped with 5 mm triple resonance single axis gradient probe and a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	H1-47 subunit A ATP synthase	[U-99% 13C; U-99% 15N]		0.5 - 1 mM
2	sodium azide	natural abundance		0.1 %
3	H2O	natural abundance		90 %
4	D2O	[U-100% 2H]		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15870_2k6i.nef
Input source #2: Coordindates	2k6i.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-------
MKHHHHHHPMGVSVMEAIKEVKLAEEQAVKEIEEAKNRAEQIKAEAIEEAKKLIAC
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKHHHHHHPMGVSVMEAIKEVKLAEEQAVKEIEEAKNRAEQIKAEAIEEAKKLIAC
--------10--------20--------30--------40--------50------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	56	0	0	100.0

Content subtype: combined_15870_2k6i.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	487		83.9 (chain: A, length: 56)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	693 (1)	noe	83.9 (chain: A, length: 56)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	58 (58)	.	64.3 (chain: A, length: 56)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 83.9%
- Total number of assignments
  - ¹H chemical shifts: 278
  - ¹³C chemical shifts: 160
  - ¹⁵N chemical shifts: 49
- 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: 56, Sequence coverage: 83.9%
- Total number of restraints: 693
- Weight of restraints: 1.0 (693)
- Potential type of restraints: upper-bound-parabolic (693)
- Range of distance target values: 2.86, 5.5 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 64.3%
- Total number of restraints: 58
- Total number of restraints per polymer type: 58
- Weight of restraints: 1.0 (58)
- Potential type of restraints: square-well-parabolic (58)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords archaeal ATPase, F1FO ATP synthase, Methanocaldococcus jannaschii, nuclear magnetic resonance, V1VO ATPase