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Open Dataset XSDUNFBU


Unraveling conformational changes behind electron bifurcation in the electron-transferring flavoprotein-menaquinone oxidoreductase ABCX

Abstract:

SEC-SAXS was collected on the SIBYLS beamline (BL 12.3.1) of the ALS at LBNL to observe changes in conformation of the electron-transferring flavoprotein-menaquinone oxidoreductase ABCX (EtfABCX) of Thermotoga maritima (Tma). EtfABCX is expected to undergo various conformational shifts during its electron transfer events in order to accomplish electron bifurcation, a newly identified form of energy conservation that yields reduced ferredoxin. The enzyme complex was separated from aggregate species using in-line SEC prior to MALS and SAXS data collection and was measured in varying reduction-oxidation (redox) states with the addition of dithionite and NADH.

Experimental description:

The SEC-SAXS system was equilibrated with anaerobic buffer containing DTT overnight to scrub residual oxygen before equilibration with anaerobic buffer with or without experimental reducing agents. Sample was prepared in an anaerobic glovebox and sealed in autoloader plate prior to injection for SEC. UV-visible absorbance data was collected during sample separation as well as differential refractive index. Sample injections were of 55 uL and contained 3 mg/mL protein in 25 mM HEPES, pH 7, 200 mM NaCl, and 0.006% Tween-20. Reductant concentrations included 200 uM NADH and 183 uM dithionite. The beamline configuration followed a 2 m sample-to-detector distance with a 1.127 angstrom X-ray wavelength.

File description:

Merged I(q) versus q (A^-1) data files are uploaded as .dat files as generated in Scatter or BioXTAS RAW softwares following their processing from SEC-SAXS datasets.

Data collection technique:

SEC-SAXS

Wavelength

1.23984 Å

Sample to Detector Distance

2.0 m


Created: 2022-07-16

Updated: 2022-10-18

Submitting Author:

Dan Murray

Lawrence Berkeley National Laboratory, The SIBYLS Beamline

United States of America

[email protected]

Collaborators:

Experiment team includes collaborators from University of Georgia: Gerrit J. Schut, Grace Ge, and Michael W. W. Adams

Project Leader:

Greg Hura

[email protected]


Data Download Terms:

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Complete Set of SAXS Data Files:

The complete SAXS dataset is downloadable as a zip file.

  • EtfABCX_simplescattering_July2022.zip Download


Sample SAXS Data Files (total 4):

These are individual SAXS data files that are included in the complete dataset, but are available separately for quick download as examples of what is contained in the zip file.


Supplemental Data and Supporting Materials (total 0):

These data and materials may include X-ray crystal structure coordinates, multi-angle light scattering data, .etc. It may also include additional details or methods pertaining to the SAXS experiments, or the researcher's interpretations of the results.


Open SAXS data analysis sites in a new tab using these links:

SAXS Similarity SAXS FrameSlice


Samples:

  • Macromolecule 1: EcABCX2C
    • Sample Full Name: 9x His-tagged Thermotoga maritima electron-transferring flavoprotein-menaquinone oxidoreductase ABCX expressed in Escherichia coli
    • Sample Type: Protein
    • Source Organism: Thermotoga maritima
    • Source Organism NCBI Taxonomy ID: 2336
    • Expression System: E. coli
    • Expression NCBI Taxonomy ID: 562
    • Sequence or Chemical Formula:
    • >7KOE_1|Chains A, E|Electron transfer flavoprotein, beta subunit|Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (243274) MAHHHHHHHHHANVVVCIKQVPDTTNVRIDRKTNNLVREGVPSIINPDDERALELASQLKEKFGATVYVITMGPPQAKEALKDAIAFGLDEAVHLSDRTFAGADTLATTYTLYWGIKKIEERIGKIDLILTGKQAVDGDTGQVGPGLATRFGYALGAYVVRIEEIDPEKKEMVIVRRLDQGFEKIRLKLPAVLTITDELNKPRYADLPNLIRAIRYEPIVWTHKDLGLDPKKCGFFGSPTRVVSTNIPPARKGGDIISKNEDPEVAAEKLIEALKKFEAVRLVEALKPVLEGEKDE >7KOE_2|Chains B, F|Electron transfer flavoprotein, alpha subunit|Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (243274) MSEKKIIFVLIEHHGGKAHPVSWELIGKARDLASKLENSEVWGVLLGEGLESVAKEAIQRGADKVLYVKNREFNTYVNYLYKKALVDMVRKYRPEIFLIGATLEGRELAGMVATELETGLTADCTGLDIIPDKKLLAMTRPTFGGNLMATIMCPDHRPQMATVRPGVMKELPPDPERTGEIIEEEYDLGTFDKLIEILETIPLQTQVNLEYAPVVVAGGKGVGGPEGFKKLKELADLLGGEVGASRAAVKAGWISPEHQVGQTGKTVRPVLYFACGISGAIQHVVGIKESEIIVAINIDEKAPIFDIADIGIVGDLHKVVPALTAKLRELLNKSGVKK >7KOE_3|Chains C, G|Electron transfer flavoprotein-quinone oxidoreductase FixC|Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (243274) MKIEFDVVVVGAGPSGLSCAYVLAKNGLKVAVVEKGEYPGSKNVMGGVLYVHPLKEIMPDFLEKAANSKALERNVIEQNLWLLGNEGVIKIGHRNVEWKENPNAFTVLRANFDRWFAQEVEKAGALIIPKTKVEDFLRNEKGEIAGVVTSRPKGEIHSKAVVIAEGVNPILTMKAGLRKEDLKPHMVAVAVKEVISVPEDVVNRVFGVEGNDGATIELLGSWSEGMFGMGFLYANRSSVSLGCGVLLEDLRKKKIKPYQLLENLKNHPVISDMLGEYRNNTMEYLAHLIPEGGYYAMPKVYGDRVLVCGDAAMLVNSIHREGSNHAITSGRLAAETLLEAFEKGDFSEKILKNYYLRLKESFILKDLEKYKDLMPTMEKNHQFVEIYPDLANDALKRFLQVDGTPKWDVQKQIADMVLSRRSLIGISLDLLRFWRAVR >7KOE_4|Chains D, H|Ferredoxin-like protein|Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (243274) MRIEDKLYLNRYRTDEENPHLKIKDESICAEKCSDRPCVSCCPADVYEWTESGMEVKFEGCLECGTCRIVCPFGNIEWNYPRGNYGVLYKFG
  • Macromolecule 2: EtfABCX_10EqDT
    • Sample Full Name: 9x His-tagged Thermotoga maritima electron-transferring flavoprotein-menaquinone oxidoreductase ABCX expressed in Pyrococcus furiosus with 10 Equivalents of dithionite
    • Sample Type: Protein
    • Source Organism: Thermotoga maritima
    • Source Organism NCBI Taxonomy ID: 2336
    • Expression System: E. coli
    • Expression NCBI Taxonomy ID: 562
    • Sequence or Chemical Formula:
    • >7KOE_1|Chains A, E|Electron transfer flavoprotein, beta subunit|Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (243274) MAHHHHHHHHHANVVVCIKQVPDTTNVRIDRKTNNLVREGVPSIINPDDERALELASQLKEKFGATVYVITMGPPQAKEALKDAIAFGLDEAVHLSDRTFAGADTLATTYTLYWGIKKIEERIGKIDLILTGKQAVDGDTGQVGPGLATRFGYALGAYVVRIEEIDPEKKEMVIVRRLDQGFEKIRLKLPAVLTITDELNKPRYADLPNLIRAIRYEPIVWTHKDLGLDPKKCGFFGSPTRVVSTNIPPARKGGDIISKNEDPEVAAEKLIEALKKFEAVRLVEALKPVLEGEKDE >7KOE_2|Chains B, F|Electron transfer flavoprotein, alpha subunit|Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (243274) MSEKKIIFVLIEHHGGKAHPVSWELIGKARDLASKLENSEVWGVLLGEGLESVAKEAIQRGADKVLYVKNREFNTYVNYLYKKALVDMVRKYRPEIFLIGATLEGRELAGMVATELETGLTADCTGLDIIPDKKLLAMTRPTFGGNLMATIMCPDHRPQMATVRPGVMKELPPDPERTGEIIEEEYDLGTFDKLIEILETIPLQTQVNLEYAPVVVAGGKGVGGPEGFKKLKELADLLGGEVGASRAAVKAGWISPEHQVGQTGKTVRPVLYFACGISGAIQHVVGIKESEIIVAINIDEKAPIFDIADIGIVGDLHKVVPALTAKLRELLNKSGVKK >7KOE_3|Chains C, G|Electron transfer flavoprotein-quinone oxidoreductase FixC|Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (243274) MKIEFDVVVVGAGPSGLSCAYVLAKNGLKVAVVEKGEYPGSKNVMGGVLYVHPLKEIMPDFLEKAANSKALERNVIEQNLWLLGNEGVIKIGHRNVEWKENPNAFTVLRANFDRWFAQEVEKAGALIIPKTKVEDFLRNEKGEIAGVVTSRPKGEIHSKAVVIAEGVNPILTMKAGLRKEDLKPHMVAVAVKEVISVPEDVVNRVFGVEGNDGATIELLGSWSEGMFGMGFLYANRSSVSLGCGVLLEDLRKKKIKPYQLLENLKNHPVISDMLGEYRNNTMEYLAHLIPEGGYYAMPKVYGDRVLVCGDAAMLVNSIHREGSNHAITSGRLAAETLLEAFEKGDFSEKILKNYYLRLKESFILKDLEKYKDLMPTMEKNHQFVEIYPDLANDALKRFLQVDGTPKWDVQKQIADMVLSRRSLIGISLDLLRFWRAVR >7KOE_4|Chains D, H|Ferredoxin-like protein|Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (243274) MRIEDKLYLNRYRTDEENPHLKIKDESICAEKCSDRPCVSCCPADVYEWTESGMEVKFEGCLECGTCRIVCPFGNIEWNYPRGNYGVLYKFG
  • Macromolecule 3: EcABCX2C_NADH
    • Sample Full Name: 9x His-tagged Thermotoga maritima electron-transferring flavoprotein-menaquinone oxidoreductase ABCX expressed in Escherichia coli with 200 uM NADH
    • Sample Type: Protein
    • Source Organism: Thermotoga maritima
    • Source Organism NCBI Taxonomy ID: 2336
    • Expression System: E. coli
    • Expression NCBI Taxonomy ID: 562
    • Sequence or Chemical Formula:
    • >7KOE_1|Chains A, E|Electron transfer flavoprotein, beta subunit|Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (243274) MAHHHHHHHHHANVVVCIKQVPDTTNVRIDRKTNNLVREGVPSIINPDDERALELASQLKEKFGATVYVITMGPPQAKEALKDAIAFGLDEAVHLSDRTFAGADTLATTYTLYWGIKKIEERIGKIDLILTGKQAVDGDTGQVGPGLATRFGYALGAYVVRIEEIDPEKKEMVIVRRLDQGFEKIRLKLPAVLTITDELNKPRYADLPNLIRAIRYEPIVWTHKDLGLDPKKCGFFGSPTRVVSTNIPPARKGGDIISKNEDPEVAAEKLIEALKKFEAVRLVEALKPVLEGEKDE >7KOE_2|Chains B, F|Electron transfer flavoprotein, alpha subunit|Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (243274) MSEKKIIFVLIEHHGGKAHPVSWELIGKARDLASKLENSEVWGVLLGEGLESVAKEAIQRGADKVLYVKNREFNTYVNYLYKKALVDMVRKYRPEIFLIGATLEGRELAGMVATELETGLTADCTGLDIIPDKKLLAMTRPTFGGNLMATIMCPDHRPQMATVRPGVMKELPPDPERTGEIIEEEYDLGTFDKLIEILETIPLQTQVNLEYAPVVVAGGKGVGGPEGFKKLKELADLLGGEVGASRAAVKAGWISPEHQVGQTGKTVRPVLYFACGISGAIQHVVGIKESEIIVAINIDEKAPIFDIADIGIVGDLHKVVPALTAKLRELLNKSGVKK >7KOE_3|Chains C, G|Electron transfer flavoprotein-quinone oxidoreductase FixC|Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (243274) MKIEFDVVVVGAGPSGLSCAYVLAKNGLKVAVVEKGEYPGSKNVMGGVLYVHPLKEIMPDFLEKAANSKALERNVIEQNLWLLGNEGVIKIGHRNVEWKENPNAFTVLRANFDRWFAQEVEKAGALIIPKTKVEDFLRNEKGEIAGVVTSRPKGEIHSKAVVIAEGVNPILTMKAGLRKEDLKPHMVAVAVKEVISVPEDVVNRVFGVEGNDGATIELLGSWSEGMFGMGFLYANRSSVSLGCGVLLEDLRKKKIKPYQLLENLKNHPVISDMLGEYRNNTMEYLAHLIPEGGYYAMPKVYGDRVLVCGDAAMLVNSIHREGSNHAITSGRLAAETLLEAFEKGDFSEKILKNYYLRLKESFILKDLEKYKDLMPTMEKNHQFVEIYPDLANDALKRFLQVDGTPKWDVQKQIADMVLSRRSLIGISLDLLRFWRAVR >7KOE_4|Chains D, H|Ferredoxin-like protein|Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (243274) MRIEDKLYLNRYRTDEENPHLKIKDESICAEKCSDRPCVSCCPADVYEWTESGMEVKFEGCLECGTCRIVCPFGNIEWNYPRGNYGVLYKFG
  • Macromolecule 4: EtfABCX
    • Sample Full Name: 9x His-tagged Thermotoga maritima electron-transferring flavoprotein-menaquinone oxidoreductase ABCX expressed in Pyrococcus furiosus
    • Sample Type: Protein
    • Source Organism: Thermotoga maritima
    • Source Organism NCBI Taxonomy ID: 2336
    • Expression System: E. coli
    • Expression NCBI Taxonomy ID: 562
    • Sequence or Chemical Formula:
    • >7KOE_1|Chains A, E|Electron transfer flavoprotein, beta subunit|Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (243274) MAHHHHHHHHHANVVVCIKQVPDTTNVRIDRKTNNLVREGVPSIINPDDERALELASQLKEKFGATVYVITMGPPQAKEALKDAIAFGLDEAVHLSDRTFAGADTLATTYTLYWGIKKIEERIGKIDLILTGKQAVDGDTGQVGPGLATRFGYALGAYVVRIEEIDPEKKEMVIVRRLDQGFEKIRLKLPAVLTITDELNKPRYADLPNLIRAIRYEPIVWTHKDLGLDPKKCGFFGSPTRVVSTNIPPARKGGDIISKNEDPEVAAEKLIEALKKFEAVRLVEALKPVLEGEKDE >7KOE_2|Chains B, F|Electron transfer flavoprotein, alpha subunit|Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (243274) MSEKKIIFVLIEHHGGKAHPVSWELIGKARDLASKLENSEVWGVLLGEGLESVAKEAIQRGADKVLYVKNREFNTYVNYLYKKALVDMVRKYRPEIFLIGATLEGRELAGMVATELETGLTADCTGLDIIPDKKLLAMTRPTFGGNLMATIMCPDHRPQMATVRPGVMKELPPDPERTGEIIEEEYDLGTFDKLIEILETIPLQTQVNLEYAPVVVAGGKGVGGPEGFKKLKELADLLGGEVGASRAAVKAGWISPEHQVGQTGKTVRPVLYFACGISGAIQHVVGIKESEIIVAINIDEKAPIFDIADIGIVGDLHKVVPALTAKLRELLNKSGVKK >7KOE_3|Chains C, G|Electron transfer flavoprotein-quinone oxidoreductase FixC|Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (243274) MKIEFDVVVVGAGPSGLSCAYVLAKNGLKVAVVEKGEYPGSKNVMGGVLYVHPLKEIMPDFLEKAANSKALERNVIEQNLWLLGNEGVIKIGHRNVEWKENPNAFTVLRANFDRWFAQEVEKAGALIIPKTKVEDFLRNEKGEIAGVVTSRPKGEIHSKAVVIAEGVNPILTMKAGLRKEDLKPHMVAVAVKEVISVPEDVVNRVFGVEGNDGATIELLGSWSEGMFGMGFLYANRSSVSLGCGVLLEDLRKKKIKPYQLLENLKNHPVISDMLGEYRNNTMEYLAHLIPEGGYYAMPKVYGDRVLVCGDAAMLVNSIHREGSNHAITSGRLAAETLLEAFEKGDFSEKILKNYYLRLKESFILKDLEKYKDLMPTMEKNHQFVEIYPDLANDALKRFLQVDGTPKWDVQKQIADMVLSRRSLIGISLDLLRFWRAVR >7KOE_4|Chains D, H|Ferredoxin-like protein|Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (243274) MRIEDKLYLNRYRTDEENPHLKIKDESICAEKCSDRPCVSCCPADVYEWTESGMEVKFEGCLECGTCRIVCPFGNIEWNYPRGNYGVLYKFG