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11 hits found for Oda

SASDJ73 – Ubiquitin-like UHRF1 with PHD and RING finger domains (TTD-L2 (123-301))

E3 ubiquitin-protein ligase UHRF1 experimental SAS data
E3 ubiquitin-protein ligase UHRF1 Kratky plot
Sample: E3 ubiquitin-protein ligase UHRF1 monomer, 21 kDa Homo sapiens protein
Buffer: SAXS Buffer, pH: 7.5
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2018 Nov 26
Serine 298 Phosphorylation in Linker 2 of UHRF1 Regulates Ligand-Binding Property of its Tandem Tudor Domain Journal of Molecular Biology (2020)
...Oda T, Unoki M, Ikeguchi M, Arita K
RgGuinier 2.0 nm
Dmax 6.6 nm
VolumePorod 26 nm3

SASDJ83 – Phosphorylated ubiquitin-like UHRF1 with PHD and RING finger domains (phTTD-L2 (123-301)

E3 ubiquitin-protein ligase UHRF1 experimental SAS data
E3 ubiquitin-protein ligase UHRF1 Kratky plot
Sample: E3 ubiquitin-protein ligase UHRF1 monomer, 21 kDa Homo sapiens protein
Buffer: SAXS buffer, pH: 7.5
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2018 Nov 26
Serine 298 Phosphorylation in Linker 2 of UHRF1 Regulates Ligand-Binding Property of its Tandem Tudor Domain Journal of Molecular Biology (2020)
...Oda T, Unoki M, Ikeguchi M, Arita K
RgGuinier 2.1 nm
Dmax 7.0 nm
VolumePorod 29 nm3

SASDWA3 – Ovalbumin, Monomer from SEC-SANS

Ovalbumin experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Ovalbumin monomer, 43 kDa Gallus gallus protein
Buffer: 100 mM Tris-HCl, 100 mM NaCl in 100% v/v D₂O, pH: 7.5
Experiment: SANS data collected at SANS-U, JRR-3 (Japan Atomic Energy Agency) on 2024 Apr 22
Size-exclusion chromatography–small-angle neutron scattering system optimized for an instrument with medium neutron flux Journal of Applied Crystallography 58(2) (2025)
...Oda T, Mayumi K, Sugiyama M
RgGuinier 2.0 nm
Dmax 6.5 nm

SASDWB3 – Bovine serum albumin, monomer from SEC-SANS

Albumin (natural variant A214T) experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Albumin (natural variant A214T) monomer, 66 kDa Bos taurus protein
Buffer: 100 mM Tris-HCl, 100 mM NaCl in 100% v/v D₂O, pH: 7.5
Experiment: SANS data collected at SANS-U, JRR-3 (Japan Atomic Energy Agency) on 2024 Apr 22
Size-exclusion chromatography–small-angle neutron scattering system optimized for an instrument with medium neutron flux Journal of Applied Crystallography 58(2) (2025)
...Oda T, Mayumi K, Sugiyama M
RgGuinier 2.6 nm
Dmax 8.7 nm

SASDWC3 – Apoferritin, from SEC-SANS

Ferritin light chain experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Ferritin light chain 24-mer, 476 kDa Equus caballus protein
Buffer: 100 mM Tris-HCl, 100 mM NaCl in 100% v/v D₂O, pH: 7.5
Experiment: SANS data collected at SANS-U, JRR-3 (Japan Atomic Energy Agency) on 2024 Apr 22
Size-exclusion chromatography–small-angle neutron scattering system optimized for an instrument with medium neutron flux Journal of Applied Crystallography 58(2) (2025)
...Oda T, Mayumi K, Sugiyama M
RgGuinier 5.4 nm
Dmax 23.1 nm

SASDWD3 – Cyanobacterial circadian clock protein KaiB-KaiC complex (hydrogenated-KaiB and hydrogenated-KaiC in 100% v/v D₂O ) measured by SEC-SANS

Circadian clock oscillator protein KaiBCircadian clock oscillator protein KaiC experimental SAS data
Circadian clock oscillator protein KaiB Circadian clock oscillator protein KaiC Kratky plot
Sample: Circadian clock oscillator protein KaiB hexamer, 71 kDa Synechococcus sp. (strain … protein
Circadian clock oscillator protein KaiC hexamer, 356 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 SANS-U, JRR-3 (Japan Atomic Energy Agency) on 2024 Jul 2
Size-exclusion chromatography–small-angle neutron scattering system optimized for an instrument with medium neutron flux Journal of Applied Crystallography 58(2) (2025)
...Oda T, Mayumi K, Sugiyama M
RgGuinier 4.9 nm
Dmax 14.4 nm

SASDWE3 – Cyanobacterial circadian clock protein KaiB-KaiC complex (71% deuterated-KaiB and hydrogenated-KaiC in 100% v/v D₂O ) measured by SEC-SANS

Circadian clock oscillator protein KaiBCircadian clock oscillator protein KaiC experimental SAS data
Circadian clock oscillator protein KaiB Circadian clock oscillator protein KaiC Kratky plot
Sample: Circadian clock oscillator protein KaiB hexamer, 71 kDa Synechococcus sp. (strain … protein
Circadian clock oscillator protein KaiC hexamer, 356 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 SANS-U, JRR-3 (Japan Atomic Energy Agency) on 2024 Jul 2
Size-exclusion chromatography–small-angle neutron scattering system optimized for an instrument with medium neutron flux Journal of Applied Crystallography 58(2) (2025)
...Oda T, Mayumi K, Sugiyama M
RgGuinier 4.3 nm
Dmax 11.7 nm

SASDWF3 – Circadian clock protein KaiC (hydrogenated-KaiC in 100% v/v D₂O ) measured by SEC-SANS

Circadian clock oscillator protein KaiC experimental SAS data
Circadian clock oscillator protein KaiC Kratky plot
Sample: Circadian clock oscillator protein KaiC hexamer, 356 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 SANS-U, JRR-3 (Japan Atomic Energy Agency) on 2024 Jul 2
Size-exclusion chromatography–small-angle neutron scattering system optimized for an instrument with medium neutron flux Journal of Applied Crystallography 58(2) (2025)
...Oda T, Mayumi K, Sugiyama M
RgGuinier 4.4 nm
Dmax 11.9 nm

SASDEH3 – TubR protein of the pXO1-like plasmid pBc10987 from B. cereus (Bc-TubR) bound to S48 DNA (Bc-TubR : S48 DNA complex)

S48 DNA strand 1S48 DNA strand 2TubR of the pXO1-like plasmid pBc10987 from B. cereus (Bc-TubR) experimental SAS data
MOLECULAR DYNAMICS FRAME model
Sample: S48 DNA strand 1 monomer, 21 kDa DNA
S48 DNA strand 2 monomer, 21 kDa DNA
TubR of the pXO1-like plasmid pBc10987 from B. cereus (Bc-TubR) decamer, 137 kDa protein
Buffer: 0.1 M NaCl, 10 mM Tris, pH: 8
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2017 Nov 28
Cooperative DNA Binding of the Plasmid Partitioning Protein TubR from the Bacillus cereus pXO1 Plasmid. J Mol Biol (2018)
...Oda T, Sato M, Fuchigami S
RgGuinier 6.1 nm
Dmax 23.0 nm
VolumePorod 305 nm3

SASDE99 – Calredoxin with EGTA

Calredoxin, Redox protein from Chlamydomonas reinhardtii experimental SAS data
Calredoxin, Redox protein from Chlamydomonas reinhardtii Kratky plot
Sample: Calredoxin, Redox protein from Chlamydomonas reinhardtii monomer, 40 kDa Chlamydomonas reinhardtii protein
Buffer: 20 mM Tris, 150 mM NaCl, 1 mM DTT, 5 mM EGTA, pH: 8
Experiment: SAXS data collected at Rigaku BioSAXS-1000, Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University on 2015 Nov 17
Calcium sensing via EF-hand 4 enables thioredoxin activity in the sensor-responder protein calredoxin in the green alga Chlamydomonas reinhardtii. J Biol Chem (2019)
...Oda T, Sato M, Hippler M, Kurisu G
RgGuinier 2.5 nm
Dmax 8.7 nm
VolumePorod 60 nm3

SASDEA9 – Calredoxin with Calcium

Calredoxin, Redox protein from Chlamydomonas reinhardtii experimental SAS data
Calredoxin, Redox protein from Chlamydomonas reinhardtii Kratky plot
Sample: Calredoxin, Redox protein from Chlamydomonas reinhardtii monomer, 40 kDa Chlamydomonas reinhardtii protein
Buffer: 20 mM Tris, 150 mM NaCl, 1 mM DTT, 5 mM CaCl2, pH: 8
Experiment: SAXS data collected at Rigaku BioSAXS-1000, Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University on 2015 Nov 17
Calcium sensing via EF-hand 4 enables thioredoxin activity in the sensor-responder protein calredoxin in the green alga Chlamydomonas reinhardtii. J Biol Chem (2019)
...Oda T, Sato M, Hippler M, Kurisu G
RgGuinier 3.1 nm
Dmax 11.6 nm
VolumePorod 68 nm3