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- PDB-2lx5: NMR solution structure of peptide epsilon(103-120) from Mycobacte... -

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Basic information

Entry
Database: PDB / ID: 2lx5
TitleNMR solution structure of peptide epsilon(103-120) from Mycobacterium tuberculosis F-ATPsynthase
ComponentsATP synthase epsilon chain
KeywordsHYDROLASE INHIBITOR / F-ATPsynthase / epsilon subunit / alpha helix / coupling subunit
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 / ATP synthase epsilon chain
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsBasak, S. / Rishikesan, S. / Gruber, G.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2013
Title: Variations of Subunit {varepsilon} of the Mycobacterium tuberculosis F1Fo ATP Synthase and a Novel Model for Mechanism of Action of the Tuberculosis Drug TMC207.
Authors: Biukovic, G. / Basak, S. / Manimekalai, M.S. / Rishikesan, S. / Roessle, M. / Dick, T. / Rao, S.P. / Hunke, C. / Gruber, G.
History
DepositionAug 14, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
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)1,9241
Polymers1,9241
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 1924.284 Da / Num. of mol.: 1 / Fragment: UNP residues 103-120 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria) / References: UniProt: P63662, UniProt: P9WPV1*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 2 mM epsilon103, 50 % [U-99% 2H] TFE, 25 mM sodium phosphate, 300 mM sodium chloride, trifluoroethanol/water
Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMepsilon103-120-11
50 %TFE-2[U-99% 2H]1
25 mMsodium phosphate-31
300 mMsodium chloride-41
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 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
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardchemical shift calculation
SparkyGoddarddata analysis
SparkyGoddardpeak picking
TALOSCornilescu, Delaglio and Baxgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsProtein phi angle constraints total count: 9 / Protein psi angle constraints total count: 9
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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