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- PDB-2ov6: The NMR structure of subunit F of the Methanogenic A1Ao ATP synth... -

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Basic information

Entry
Database: PDB / ID: 2ov6
TitleThe NMR structure of subunit F of the Methanogenic A1Ao ATP synthase and its interaction with the nucleotide-binding subunit B
ComponentsV-type ATP synthase subunit F
KeywordsHYDROLASE / F subunit / A1Ao ATP synthase
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase activity, rotational mechanism / ATP binding
Similarity search - Function
ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F, bacterial/archaeal / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase (F/14-kDa) subunit / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
V-type ATP synthase subunit F
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodSOLUTION NMR / Distance constraints, Simulated annealing, Molecular dynamics, Torsion angle dynamics
AuthorsGayen, S. / Subramanian, V. / Biukovic, G.
CitationJournal: Biochemistry / Year: 2007
Title: NMR solution structure of subunit F of the methanogenic A1AO adenosine triphosphate synthase and its interaction with the nucleotide-binding subunit B.
Authors: Gayen, S. / Vivekanandan, S. / Biukovic, G. / Gruber, G. / Yoon, H.S.
History
DepositionFeb 13, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: V-type ATP synthase subunit F


Theoretical massNumber of molelcules
Total (without water)10,7771
Polymers10,7771
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein V-type ATP synthase subunit F / V-type ATPase subunit F / Subunit F A1Ao ATP synthase


Mass: 10777.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Strain: Go1 / Plasmid: pET9d1-His3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q60185, H+-transporting two-sector ATPase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-edited-HSQC-NOESY
121HNCA
131HN(CA)CB
141CBCA(CO)NH
151HNCO
161(H)CCH-TOCSY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 0.5mM F subunit uniformly labeled 15N; 15N, 13C; 25mM phosphate buffer pH 6.5; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.5 / Pressure: AMBIENT / Temperature: 288 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
CYANA2.1Guentert, P.structure solution
NMRPipe2.3Delaglio, F.processing
TopSpin1.3Brukercollection
Sparky3.112Goddard, T.D.data analysis
CYANA2.1Guentert, P.refinement
RefinementMethod: Distance constraints, Simulated annealing, Molecular dynamics, Torsion angle dynamics
Software ordinal: 1
Details: Total NMR constraints 863, Torsional angle restraints 184, Hydrogen bond restraints 32
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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