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- PDB-5yio: NMR solution structure of subunit epsilon of the Mycobacterium tu... -

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Basic information

Entry
Database: PDB / ID: 5yio
TitleNMR solution structure of subunit epsilon of the Mycobacterium tuberculosis F-ATP synthase
ComponentsATP synthase epsilon chain
KeywordsPROTON TRANSPORT / Mycobacterium / F-ATP synthase / subunit epsilon / bioenergetics / tuberculosis
Function / homology
Function and homology information


proton motive force-driven ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / proton-transporting ATP synthase activity, rotational mechanism / peptidoglycan-based cell wall / ATP binding / plasma membrane
Similarity search - Function
ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain
Similarity search - Domain/homology
ATP synthase epsilon chain
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsShin, J. / Ragunathan, P. / Sundararaman, L. / Nartey, W. / Manimekalai, M.S.S. / Bogdanovic, N. / Gruber, G.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Health (MOH), SingaporeCBRG12nov049 Singapore
CitationJournal: FEBS J. / Year: 2018
Title: The NMR solution structure of Mycobacterium tuberculosis F-ATP synthase subunit epsilon provides new insight into energy coupling inside the rotary engine.
Authors: Joon, S. / Ragunathan, P. / Sundararaman, L. / Nartey, W. / Kundu, S. / Manimekalai, M.S.S. / Bogdanovic, N. / Dick, T. / Gruber, G.
History
DepositionOct 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _entity.formula_weight
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 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 epsilon chain


Theoretical massNumber of molelcules
Total (without water)13,1501
Polymers13,1501
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7590 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein ATP synthase epsilon chain / ATP synthase F1 sector epsilon subunit / F-ATPase epsilon subunit


Mass: 13149.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: atpC, Rv1311, MTCY373.31 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WPV1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic13D 1H-15N NOESY
132isotropic23D 1H-13C NOESY
142isotropic23D (H)CCH-TOCSY
152isotropic23D HN(CA)CB
162isotropic23D CBCA(CO)NH
172isotropic23D HNCA
182isotropic23D HN(CO)CA
193isotropic23D 1H-13C NOESY
1103isotropic23D (H)CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.4 mM [U-15N] subunit epsilon of the Mycobacterium tuberculosis F-ATP synthase, 90% H2O/10% D2O15N90% H2O/10% D2O
solution20.4 mM [U-13C; U-15N] subunit epsilon of the Mycobacterium tuberculosis F-ATP synthase, 90% H2O/10% D2OU-13C/15N_190% H2O/10% D2O
solution30.4 mM [U-13C; U-15N] subunit epsilon of the Mycobacterium tuberculosis F-ATP synthase, 100% D2OU-13C/15N_2100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMsubunit epsilon of the Mycobacterium tuberculosis F-ATP synthase[U-15N]1
0.4 mMsubunit epsilon of the Mycobacterium tuberculosis F-ATP synthase[U-13C; U-15N]2
0.4 mMsubunit epsilon of the Mycobacterium tuberculosis F-ATP synthase[U-13C; U-15N]3
Sample conditionsIonic strength: 200mM NaCl mM / Label: condition_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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