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- PDB-7xkz: Solution structure of subunit epsilon of the Mycobacterium absces... -

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Basic information

Entry
Database: PDB / ID: 7xkz
TitleSolution structure of subunit epsilon of the Mycobacterium abscessus F-ATP synthase
ComponentsATP synthase epsilon chain
KeywordsELECTRON TRANSPORT / Mycobacteria / F-ATP synthase / bioenergetics / oxidative phosphorylation
Function / homologyATP 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 / proton-transporting ATP synthase complex, catalytic core F(1) / proton-transporting ATP synthase activity, rotational mechanism / ATP binding / plasma membrane / ATP synthase epsilon chain
Function and homology information
Biological speciesMycobacteroides abscessus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsShin, J. / Grueber, G. / Harikishore, A. / Wong, C.F. / Prya, R. / Dick, T.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRFCRP18201701 Singapore
CitationJournal: Febs J. / Year: 2022
Title: Atomic solution structure of Mycobacterium abscessus F-ATP synthase subunit epsilon and identification of Ep1MabF1 as a targeted inhibitor.
Authors: Shin, J. / Harikishore, A. / Wong, C.F. / Ragunathan, P. / Dick, T. / Gruber, G.
History
DepositionApr 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1May 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)13,9031
Polymers13,9031
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

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


Mass: 13903.489 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus (bacteria) / Gene: atpC, D2E76_04560, ERS075656_01892 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U0YP27

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic13D HN(CA)CB
132isotropic13D CBCA(CO)NH
142isotropic13D HNCA
152isotropic13D HN(CO)CA
162isotropic13D HNCO
172isotropic13D (H)CCH-TOCSY
182isotropic13D 1H-15N NOESY
192isotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-15N] Mycobacterium abscessus F-ATP synthase subunit epsilon, 50 mM TRIS, 150 mM sodium chloride, 0.01 % v/v sodium azide, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.5 mM [U-100% 13C; U-100% 15N] Mycobacterium abscessus F-ATP synthase subunit epsilon, 50 mM TRIS, 150 mM sodium chloride, 0.01 % v/v sodium azide, 90% H2O/10% D2O13C_15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMMycobacterium abscessus F-ATP synthase subunit epsilon[U-15N]1
50 mMTRISnatural abundance1
150 mMsodium chloridenatural abundance1
0.01 % v/vsodium azidenatural abundance1
0.5 mMMycobacterium abscessus F-ATP synthase subunit epsilon[U-100% 13C; U-100% 15N]2
50 mMTRISnatural abundance2
150 mMsodium chloridenatural abundance2
0.01 % v/vsodium azidenatural abundance2
Sample conditionsIonic strength: 150 mM / Label: condition_1 / pH: 7.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, 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: 6
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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