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- PDB-2kpb: Specific motifs of the V-ATPase a2-subunit isoform interact with ... -

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Basic information

Entry
Database: PDB / ID: 2kpb
TitleSpecific motifs of the V-ATPase a2-subunit isoform interact with catalytic and regulatory domains of ARNO
ComponentsARNO-p(375-400)
KeywordsHYDROLASE / ARNO PB domain
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 5
AuthorsMerkulova, M. / Bakulina, A. / Thaker, Y.R. / Gr ber, G. / Marshansky, V.
CitationJournal: Biochim.Biophys.Acta / Year: 2010
Title: Specific motifs of the V-ATPase a2-subunit isoform interact with catalytic and regulatory domains of ARNO
Authors: Merkulova, M. / Bakulina, A. / Thaker, Y.R. / Gruber, G. / Marshansky, V.
History
DepositionOct 11, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 2, 2010Provider: 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
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 1.3May 29, 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: ARNO-p(375-400)


Theoretical massNumber of molelcules
Total (without water)3,0841
Polymers3,0841
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)20 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide ARNO-p(375-400)


Mass: 3083.667 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized peptide

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: ARNO peptide from 375-400 amino acids with phosphorylated Ser392
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 1-2mM ARNO-p(375-400)-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleUnits: mM / Component: ARNO-p(375-400)-1 / Conc. range: 1-2
Sample conditionsTemperature: 298 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
CYANA2.1structure solution
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Representative conformer: 1

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