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- PDB-1pyv: NMR solution structure of the mitochondrial F1b presequence pepti... -

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Basic information

Entry
Database: PDB / ID: 1pyv
TitleNMR solution structure of the mitochondrial F1b presequence peptide from Nicotiana plumbaginifolia
ComponentsATP synthase beta chain, mitochondrial precursor
KeywordsHYDROLASE
Function / homology
Function and homology information


: / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP hydrolysis activity / ATP binding
Similarity search - Function
ATP synthase, F1 beta subunit / ATP synthase, F1 beta subunit / ATP synthase F1 beta subunit / ATP synthase, F1 complex, beta subunit / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. ...ATP synthase, F1 beta subunit / ATP synthase, F1 beta subunit / ATP synthase F1 beta subunit / ATP synthase, F1 complex, beta subunit / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Arc Repressor Mutant, subunit A / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ATP synthase subunit beta, mitochondrial
Similarity search - Component
Biological speciesNicotiana plumbaginifolia (curled-leaved tobacco)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMoberg, P. / Nilsson, S. / Stahl, A. / Eriksson, A.C. / Glaser, E. / Maler, L.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: NMR solution structure of the mitochondrial F1beta presequence from Nicotiana plumbaginifolia
Authors: Moberg, P. / Nilsson, S. / Stahl, A. / Eriksson, A.C. / Glaser, E. / Maler, L.
History
DepositionJul 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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
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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP synthase beta chain, mitochondrial precursor


Theoretical massNumber of molelcules
Total (without water)5,7541
Polymers5,7541
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)24 / 100combination of lowest energy and restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein ATP synthase beta chain, mitochondrial precursor / F1b presequence peptide


Mass: 5753.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana plumbaginifolia (curled-leaved tobacco)
Gene: ATPB OR ATP2-1 / Plasmid: pET21d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): bl21(de3)
References: UniProt: P17614, 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
1112D NOESY
1212D TOCSY
131DQF-COSY

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Sample preparation

DetailsContents: 1 mM F1b presequence, 300 mM sodium dodecyl phosphate, 30 ul D2O
Solvent system: 30 ul D2O
Sample conditionsIonic strength: 300 mM SDS / pH: 7 / Pressure: ambient / Temperature: 318 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
Felix2000.1Accelrysdata analysis
DYANA1.5Guntert, P.structure solution
DYANA1.5Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The structure is based on a total of 539 restraints: 518 NOE-derived distance constraints, and 21 phi dihedral angle restraints from J-couplings.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: combination of lowest energy and restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 24

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