Browse by MODEL: Ab initio only

SASDML8 – Sulfite reductase hemoprotein

Sulfite reductase [NADPH] hemoprotein beta-component (Assimilatory NADPH-dependent sulfite reductase hemoprotein) experimental SAS data
Sample: Sulfite reductase [NADPH] hemoprotein beta-component (Assimilatory NADPH-dependent sulfite reductase hemoprotein) monomer, 64 kDa Escherichia coli (strain … protein
Buffer: 50 mM KPi, 100 mM NaCl, 1 mM EDTA, pH: 7.8
Experiment: SANS data collected at EQ-SANS (BL-6), Spallation Neutron Source on 2018 Jul 13
Neutron scattering maps the higher-order assembly of NADPH-dependent assimilatory sulfite reductase. Biophys J (2022)
Murray DT, Walia N, Weiss KL, Stanley CB, Randolph PS, Nagy G, Stroupe ME
RgGuinier 2.3 nm
Dmax 7.2 nm
VolumePorod 71 nm3

SASDMM8 – Reconstituted sulfite reductase dodecamer with partially deuterated hemoprotein in 0% D2O

Sulfite reductase [NADPH] hemoprotein beta-componentSulfite reductase [NADPH] flavoprotein alpha-component (His-tagged) experimental SAS data
Sample: Sulfite reductase [NADPH] hemoprotein beta-component tetramer, 256 kDa Escherichia coli (strain … protein
Sulfite reductase [NADPH] flavoprotein alpha-component (His-tagged) octamer, 565 kDa Escherichia coli (strain … protein
Buffer: 50 mM KPi, 100 mM NaCl, 1 mM EDTA, pH: 7.8
Experiment: SANS data collected at EQ-SANS (BL-6), Spallation Neutron Source on 2021 Apr 3
Neutron scattering maps the higher-order assembly of NADPH-dependent assimilatory sulfite reductase. Biophys J (2022)
Murray DT, Walia N, Weiss KL, Stanley CB, Randolph PS, Nagy G, Stroupe ME
RgGuinier 11.2 nm
Dmax 30.5 nm

SASDMP8 – Reconstituted sulfite reductase dodecamer with partially deuterated hemoprotein in 41% D2O

Sulfite reductase [NADPH] hemoprotein beta-componentSulfite reductase [NADPH] flavoprotein alpha-component (His-tagged) experimental SAS data
Sample: Sulfite reductase [NADPH] hemoprotein beta-component tetramer, 256 kDa Escherichia coli (strain … protein
Sulfite reductase [NADPH] flavoprotein alpha-component (His-tagged) octamer, 565 kDa Escherichia coli (strain … protein
Buffer: 50 mM KPi, 100 mM NaCl, 1 mM EDTA, pH: 7.8
Experiment: SANS data collected at EQ-SANS (BL-6), Spallation Neutron Source on 2021 Apr 3
Neutron scattering maps the higher-order assembly of NADPH-dependent assimilatory sulfite reductase. Biophys J (2022)
Murray DT, Walia N, Weiss KL, Stanley CB, Randolph PS, Nagy G, Stroupe ME
RgGuinier 11.4 nm
Dmax 28.5 nm
VolumePorod 417 nm3

SASDMQ8 – Reconstituted sulfite reductase dodecamer with partially deuterated hemoprotein in 86% D2O

Sulfite reductase [NADPH] hemoprotein beta-componentSulfite reductase [NADPH] flavoprotein alpha-component (His-tagged) experimental SAS data
Sample: Sulfite reductase [NADPH] hemoprotein beta-component tetramer, 256 kDa Escherichia coli (strain … protein
Sulfite reductase [NADPH] flavoprotein alpha-component (His-tagged) octamer, 565 kDa Escherichia coli (strain … protein
Buffer: 50 mM KPi, 100 mM NaCl, 1 mM EDTA, pH: 7.8
Experiment: SANS data collected at EQ-SANS (BL-6), Spallation Neutron Source on 2021 Apr 3
Neutron scattering maps the higher-order assembly of NADPH-dependent assimilatory sulfite reductase. Biophys J (2022)
Murray DT, Walia N, Weiss KL, Stanley CB, Randolph PS, Nagy G, Stroupe ME
RgGuinier 6.8 nm
Dmax 22.0 nm
VolumePorod 460 nm3

SASDKY9 – A minimal intact methyltransferase of a type I restriction-modification system

Type I restriction-modification system methyltransferase subunitProtein Ocr experimental SAS data
DAMMIF model
Sample: Type I restriction-modification system methyltransferase subunit dimer, 144 kDa Vibrio vulnificus (strain … protein
Protein Ocr dimer, 28 kDa Escherichia phage T7 protein
Buffer: 20 mM Tris-HCl,150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at 4C, Pohang Accelerator Laboratory on 2020 Apr 22
Structural features of a minimal intact methyltransferase of a type I restriction-modification system. Int J Biol Macromol (2022)
Seo PW, Hofmann A, Kim JH, Hwangbo SA, Kim JH, Kim JW, Huynh TYL, Choy HE, Kim SJ, Lee J, Lee JO, Jin KS, Park SY, Kim JS
RgGuinier 4.2 nm
Dmax 15.9 nm
VolumePorod 354 nm3

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)
Yunoki Y, Matsumoto A, Morishima K, Martel A, Porcar L, Sato N, Yogo R, Tominaga T, Inoue R, Yagi-Utsumi M, 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)
Yunoki Y, Matsumoto A, Morishima K, Martel A, Porcar L, Sato N, Yogo R, Tominaga T, Inoue R, Yagi-Utsumi M, 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

SASDLV2 – Accessory colonization factor SslE at pH 7.4

Accessory colonization factor experimental SAS data
DAMMIN model
Sample: Accessory colonization factor monomer, 160 kDa Escherichia coli (strain … protein
Buffer: 20 mM citrate-phosphate buffer, 200 mM NaCl, pH: 7.4
Experiment: SAXS data collected at B21, Diamond Light Source on 2019 Jul 27
Molecular and cellular insight into Escherichia coli SslE and its role during biofilm maturation npj Biofilms and Microbiomes 8(1) (2022)
Corsini P, Wang S, Rehman S, Fenn K, Sagar A, Sirovica S, Cleaver L, Edwards-Gayle C, Mastroianni G, Dorgan B, Sewell L, Lynham S, Iuga D, Franks W, Jarvis J, Carpenter G, Curtis M, Bernadó P, Darbari V, Garnett J
RgGuinier 4.0 nm
Dmax 14.1 nm
VolumePorod 244 nm3

SASDLW2 – Accessory colonization factor SslE at pH 4.4

Accessory colonization factor experimental SAS data
DAMMIN model
Sample: Accessory colonization factor monomer, 160 kDa Escherichia coli (strain … protein
Buffer: 20 mM citrate-phosphate buffer, 200 mM NaCl, pH: 4.4
Experiment: SAXS data collected at B21, Diamond Light Source on 2019 Jul 27
Molecular and cellular insight into Escherichia coli SslE and its role during biofilm maturation npj Biofilms and Microbiomes 8(1) (2022)
Corsini P, Wang S, Rehman S, Fenn K, Sagar A, Sirovica S, Cleaver L, Edwards-Gayle C, Mastroianni G, Dorgan B, Sewell L, Lynham S, Iuga D, Franks W, Jarvis J, Carpenter G, Curtis M, Bernadó P, Darbari V, Garnett J
RgGuinier 3.9 nm
Dmax 13.7 nm
VolumePorod 248 nm3

SASDMU6 – The N1 domain of accessory colonization factor SslE

Accessory colonization factor experimental SAS data
DAMFILT model
Sample: Accessory colonization factor monomer, 17 kDa Escherichia coli (strain … protein
Buffer: 20 mM Tris, 200 mM NaCl, pH: 8
Experiment: SAXS data collected at B21, Diamond Light Source on 2021 Apr 21
Molecular and cellular insight into Escherichia coli SslE and its role during biofilm maturation npj Biofilms and Microbiomes 8(1) (2022)
Corsini P, Wang S, Rehman S, Fenn K, Sagar A, Sirovica S, Cleaver L, Edwards-Gayle C, Mastroianni G, Dorgan B, Sewell L, Lynham S, Iuga D, Franks W, Jarvis J, Carpenter G, Curtis M, Bernadó P, Darbari V, Garnett J
RgGuinier 2.0 nm
Dmax 7.0 nm
VolumePorod 28 nm3