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- PDB-2k6i: The domain features of the peripheral stalk subunit H of the meth... -

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Basic information

Entry
Database: PDB / ID: 2k6i
TitleThe domain features of the peripheral stalk subunit H of the methanogenic A1AO ATP synthase and the NMR solution structure of H1-47
ComponentsUncharacterized protein MJ0223
KeywordsSTRUCTURAL PROTEIN / H subunit / A1AO ATP synthase / V1VO ATPase / F1FO ATP synthase / Methanocaldococcus jannaschii
Function / homologyATPase, A1A0, subunit H / : / Archaeal A-ATP synthase, subunit H, N-terminal / A-type ATP synthase subunit H
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBiukovic, N. / Gayen, S. / Pervushin, K. / Gruber, G. / Biukovic, G.
CitationJournal: Biophys.J. / Year: 2009
Title: Domain features of the peripheral stalk subunit H of the methanogenic A1AO ATP synthase and the NMR solution structure of H(1-47).
Authors: Biukovic, G. / Gayen, S. / Pervushin, K. / Gruber, G.
History
DepositionJul 9, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
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 8, 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: Uncharacterized protein MJ0223


Theoretical massNumber of molelcules
Total (without water)6,3941
Polymers6,3941
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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 Uncharacterized protein MJ0223


Mass: 6394.440 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0223 / Plasmid: pET9d1-His3 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: Q57676

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D C(CO)NH
1613D H(CCO)NH
1712D 1H-15N HSQC
1812D 1H-13C HSQC

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Sample preparation

DetailsContents: 0.5-1 mM [U-99% 13C; U-99% 15N] H1-47 subunit A ATP synthase, 0.1 % sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMH1-47 subunit A ATP synthase[U-99% 13C; U-99% 15N]1
0.1 %sodium azide1
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
Sparky3.113Goddard, T.D. et al.peak picking
Sparky3.113Goddard, T.D. et al.chemical shift assignment
CYANA3Guntert, P. et al.structure solution
TopSpin1.3Bruker Biospincollection
TopSpin1.3Bruker Biospinprocessing
TALOSCornilescu, G. et al.torsional angle calculation
CYANA3Guntert, P. et al.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 468 / NOE intraresidue total count: 133 / NOE long range total count: 0 / NOE medium range total count: 155 / NOE sequential total count: 180 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 29 / Protein psi angle constraints total count: 29
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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