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- PDB-2khk: NMR solution structure of the b30-82 domain of subunit b of Esche... -

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Basic information

Entry
Database: PDB / ID: 2khk
TitleNMR solution structure of the b30-82 domain of subunit b of Escherichia coli F1FO ATP synthase
ComponentsATP synthase subunit b
KeywordsTRANSPORT PROTEIN / b30-82 / F1FO ATP synthase / NMR spectroscopy / ATP synthesis / Cell inner membrane / Cell membrane / CF(0) / Hydrogen ion transport / Ion transport / Membrane / Transmembrane / Transport
Function / homology
Function and homology information


proton-transporting ATP synthase complex / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1580 / ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
ATP synthase subunit b
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsPriya, R. / Biukovic, G. / Gayen, S. / Vivekanandan, S. / Gruber, G.
CitationJournal: J.Bacteriol. / Year: 2009
Title: Solution structure, determined by nuclear magnetic resonance, of the b30-82 domain of subunit b of Escherichia coli F1Fo ATP synthase
Authors: Priya, R. / Biukovic, G. / Gayen, S. / Vivekanandan, S. / Gruber, G.
History
DepositionApr 8, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 15, 2009Provider: 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: ATP synthase subunit b


Theoretical massNumber of molelcules
Total (without water)5,7861
Polymers5,7861
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 / 10structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein ATP synthase subunit b / ATP synthase F(0) sector subunit b / F-type ATPase subunit b / F-ATPase subunit b / ATPase subunit I


Mass: 5785.630 Da / Num. of mol.: 1 / Fragment: residues in UNP 30-82
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABA0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D H(CCO)NH
1612D 1H-15N HSQC

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Sample preparation

DetailsContents: 1mM [U-99% 13C; U-99% 15N] subunit b 30-82-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: subunit b 30-82-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 0 / pH: 6.8 / 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
CYANA2.1P.GUNTERT ET AL.refinement
SparkyGoddardchemical shift assignment
TopSpin1.3Bruker Biospinprocessing
MOLMOLKoradi, Billeter and Wuthrichstructure solution
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: 10 / Conformers submitted total number: 10 / Representative conformer: 1

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