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- PDB-2kk7: NMR solution structure of the N terminal domain of subunit E (E1-... -

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Basic information

Entry
Database: PDB / ID: 2kk7
TitleNMR solution structure of the N terminal domain of subunit E (E1-52) of A1AO ATP synthase from Methanocaldococcus jannaschii
ComponentsV-type ATP synthase subunit E
KeywordsHYDROLASE / subunit E / Methanocaldococcus jannaschii / A1AO ATP synthase / ATP synthesis / Hydrogen ion transport / Ion transport / Transport
Function / homology
Function and homology information


proton-transporting two-sector ATPase complex, catalytic domain / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP binding
Similarity search - Function
F1F0 ATP synthase subunit B, membrane domain / F-type ATP synthase subunit B-like, membrane domain superfamily / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
V-type ATP synthase subunit E
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsGayen, S. / Balakrishna, A. / Gruber, G.
CitationJournal: J.Bioenerg.Biomembr. / Year: 2009
Title: NMR solution structure of the N-terminal domain of subunit E (E1-52) of A1AO ATP synthase from Methanocaldococcus jannaschii
Authors: Gayen, S. / Balakrishna, A.M. / Gruber, G.
History
DepositionJun 16, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: V-type ATP synthase subunit E


Theoretical massNumber of molelcules
Total (without water)5,7681
Polymers5,7681
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein V-type ATP synthase subunit E / V-ATPase subunit E


Mass: 5767.812 Da / Num. of mol.: 1 / Fragment: UNP residues 2-50
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: atpE, MJ0220 / Plasmid: pET9d / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: Q57673

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D 1H-15N NOESY

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Sample preparation

DetailsContents: 25mM sodium phosphate-1, 7% D2O-2, 0.1mM sodium azide-3, 60% TFE-4, trifluoroethanol/water
Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentSolution-ID
25 mMsodium phosphate-11
7 %D2O-21
0.1 mMsodium azide-31
60 %TFE-41
Sample conditionsIonic strength: 0 / pH: 6.5 / Pressure: AMBIENT / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1P.Guntert et al.refinement
TopSpin2.1Bruker Biospincollection
MOLMOLKoradi, Billeter, Wuthrichstructure solution
SparkyGoddardchemical shift assignment
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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