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5 hits found for Okuda

SASDNJ2 – Circadian clock KaiA-KaiB-KaiC ternary protein complex measured by SEC-SAXS

Circadian clock protein KaiACircadian clock protein KaiBCircadian clock protein kinase KaiC (S431D mutant) experimental SAS data
OTHER model
Sample: Circadian clock protein KaiA dodecamer, 393 kDa Synechococcus elongatus (strain … protein
Circadian clock protein KaiB hexamer, 71 kDa Synechococcus elongatus (strain … protein
Circadian clock protein kinase KaiC (S431D mutant) hexamer, 357 kDa Synechococcus elongatus (strain … protein
Buffer: 50 mM sodium phosphate buffer, 150 mM NaCl, 5 mM MgCl2, 0.5 mM EDTA, 1 mM ATP, 1 mM DTT, 50 mM arginine, 50 mM glutamine, pH: 7.8
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2017 Dec 8
Overall structure of fully assembled cyanobacterial KaiABC circadian clock complex by an integrated experimental-computational approach. Commun Biol 5(1):184 (2022)
...Okuda A, Shimizu M, Urade R, Terauchi K, Kono H, Yagi H, Kato K, Sugiyama M
RgGuinier 7.0 nm
Dmax 24.5 nm
VolumePorod 1650 nm3

SASDNK2 – Circadian clock hKaiA-75dKaiB-75dKaiC ternary protein complex measured by SEC-SANS in 100% D2O

75% deuterated Circadian clock protein KaiBCircadian clock protein KaiA75% deuterated Circadian clock protein kinase KaiC (S431D mutant) experimental SAS data
OTHER model
Sample: 75% deuterated Circadian clock protein KaiB hexamer, 71 kDa Synechococcus elongatus (strain … protein
Circadian clock protein KaiA dodecamer, 393 kDa Synechococcus elongatus (strain … protein
75% deuterated Circadian clock protein kinase KaiC (S431D mutant) hexamer, 357 kDa Synechococcus elongatus (strain … protein
Buffer: 50 mM sodium phosphate buffer, 150 mm NaCl, 5 mM MgCl2, 0.5 mM EDTA, 1 mM ATP, 1 mM DTT, 50 mM arginine, 50 mM glutamine, in 100% D2O, pH: 7.8
Experiment: SANS data collected at D22, Institut Laue-Langevin (ILL) on 2018 Sep 19
Overall structure of fully assembled cyanobacterial KaiABC circadian clock complex by an integrated experimental-computational approach. Commun Biol 5(1):184 (2022)
...Okuda A, Shimizu M, Urade R, Terauchi K, Kono H, Yagi H, Kato K, Sugiyama M
RgGuinier 7.8 nm
Dmax 25.6 nm
VolumePorod 1620 nm3

SASDZT8 – Wild-type version of human protein disulfide-isomerase A3 (ER-60 h(WT))

human protein disulfide-isomerase A3 experimental SAS data
human protein disulfide-isomerase A3 Kratky plot
Sample: human protein disulfide-isomerase A3 monomer, 54 kDa Homo sapiens protein
Buffer: 20 mM Tris-HCl buffer, 150 mM NaCl, 1mM CaCl2, pH: 8
Experiment: SAXS data collected at Rigaku NANOPIX, KURNS on 2024 Sep 27
Integrated analysis with iCM-SANS, SAXS and MD simulations for dynamics of multi-domain proteins Journal of Applied Crystallography 59(4):1270-1281 (2026)
Okuda A, Inoue R, Kurokawa M, Martel A, Porcar L, Osaki R, Fukuzawa K, Weiss K, Pingali S, Urade R, Sugiyama M
RgGuinier 3.2 nm

SASDZU8 – Triple mutant of protein disulfide-isomerase A3 (D122N/I124L/R363N/Y364G; ER-60 h(a-bb’-a’))

triple mutant of protein disulfide-isomerase A3 (D122N/I124L/R363N/Y364G) experimental SAS data
triple mutant of protein disulfide-isomerase A3 (D122N/I124L/R363N/Y364G) Kratky plot
Sample: triple mutant of protein disulfide-isomerase A3 (D122N/I124L/R363N/Y364G) monomer, 54 kDa Homo sapiens protein
Buffer: 20 mM Tris-HCl buffer, 150 mM NaCl, 1mM CaCl2, pH: 8
Experiment: SAXS data collected at Rigaku NANOPIX, KURNS on 2024 Sep 27
Integrated analysis with iCM-SANS, SAXS and MD simulations for dynamics of multi-domain proteins Journal of Applied Crystallography 59(4):1270-1281 (2026)
Okuda A, Inoue R, Kurokawa M, Martel A, Porcar L, Osaki R, Fukuzawa K, Weiss K, Pingali S, Urade R, Sugiyama M
RgGuinier 3.2 nm

SASDZS8 – Segmental deuterated Protein disulfide-isomerase A3 comprising three point mutations (D122N/I124L/R363N/Y364G; ER-60 h(a)-pd(bb’)-h(a’))

Protein disulfide-isomerase A3 D122N/I124L/R363N/Y364G segmental deuterated experimental SAS data
Protein disulfide-isomerase A3 D122N/I124L/R363N/Y364G segmental deuterated Kratky plot
Sample: Protein disulfide-isomerase A3 D122N/I124L/R363N/Y364G segmental deuterated monomer, 54 kDa Homo sapiens protein
Buffer: 20 mM Tris-HCl buffer, 150 mM NaCl, 1mM CaCl2, pH: 8
Experiment: SAXS data collected at Rigaku NANOPIX, KURNS on 2024 Sep 27
Integrated analysis with iCM-SANS, SAXS and MD simulations for dynamics of multi-domain proteins Journal of Applied Crystallography 59(4):1270-1281 (2026)
Okuda A, Inoue R, Kurokawa M, Martel A, Porcar L, Osaki R, Fukuzawa K, Weiss K, Pingali S, Urade R, Sugiyama M
RgGuinier 3.3 nm