Browse by ORGANISM: other species

SASDM64 – LAF + P20 nanocomposite (NP added before fibrilization)

lysozyme amyloid fibrilFe3O4 nanoparticles; nominal diameter 20 nm (hydrodynamic diameter) experimental SAS data
DAMMIN model
Sample: Lysozyme amyloid fibril, 1 kDa Gallus gallus protein
Fe3O4 nanoparticles; nominal diameter 20 nm (hydrodynamic diameter) monomer, 1 kDa
Buffer: 0.2 M glycine-HCl, 80 mM NaCl, pH: 2.2
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Nov 29
Dependence of the Nanoscale Composite Morphology of Fe3O4 Nanoparticle-Infused Lysozyme Amyloid Fibrils on Timing of Infusion: A Combined SAXS and AFM Study Molecules 26(16):4864 (2021)
Schroer M, Hu P, Tomasovicova N, Batkova M, Zakutanska K, Wu P, Kopcansky P
RgGuinier 23.6 nm
Dmax 90.0 nm

SASDM74 – LAF + P20 nanocomposite (NP added after fibrilization)

lysozyme amyloid fibrilFe3O4 nanoparticles; nominal diameter 20 nm (hydrodynamic diameter) experimental SAS data
DAMMIN model
Sample: Lysozyme amyloid fibril, 1 kDa Gallus gallus protein
Fe3O4 nanoparticles; nominal diameter 20 nm (hydrodynamic diameter) monomer, 1 kDa
Buffer: 0.2 M glycine-HCl, 80 mM NaCl, pH: 2.2
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Sep 2
Dependence of the Nanoscale Composite Morphology of Fe3O4 Nanoparticle-Infused Lysozyme Amyloid Fibrils on Timing of Infusion: A Combined SAXS and AFM Study Molecules 26(16):4864 (2021)
Schroer M, Hu P, Tomasovicova N, Batkova M, Zakutanska K, Wu P, Kopcansky P
RgGuinier 31.0 nm
Dmax 75.0 nm

SASDLQ2 – PfMDH L-lactate dehydrogenase, apo

L-lactate dehydrogenase experimental SAS data
PYMOL model
Sample: L-lactate dehydrogenase tetramer, 141 kDa Plasmodium falciparum protein
Buffer: 100 mM Na-phosphate buffer, 400 mM NaCl, pH: 7.4
Experiment: SAXS data collected at Xenocs Xeuss 2.0 with MetalJet, Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University on 2019 Jul 3
A fragment-based approach identifies an allosteric pocket that impacts malate dehydrogenase activity Communications Biology 4(1) (2021)
Reyes Romero A, Lunev S, Popowicz G, Calderone V, Gentili M, Sattler M, Plewka J, Taube M, Kozak M, Holak T, Dömling A, Groves M
RgGuinier 3.4 nm
Dmax 10.5 nm
VolumePorod 211 nm3

SASDLR2 – PfMDH L-lactate dehydrogenase bound to inhibitor 2a

L-lactate dehydrogenase experimental SAS data
DAMMIF model
Sample: L-lactate dehydrogenase tetramer, 141 kDa Plasmodium falciparum protein
Buffer: 100 mM Na-phosphate buffer, 400 mM NaCl, pH: 7.4
Experiment: SAXS data collected at Xenocs Xeuss 2.0 with MetalJet, Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University on 2019 Jul 3
A fragment-based approach identifies an allosteric pocket that impacts malate dehydrogenase activity Communications Biology 4(1) (2021)
Reyes Romero A, Lunev S, Popowicz G, Calderone V, Gentili M, Sattler M, Plewka J, Taube M, Kozak M, Holak T, Dömling A, Groves M
RgGuinier 3.4 nm
Dmax 10.5 nm
VolumePorod 244 nm3

SASDLS2 – PfMDH L-lactate dehydrogenase bound to inhibitor 6a

L-lactate dehydrogenase experimental SAS data
DAMMIF model
Sample: L-lactate dehydrogenase tetramer, 141 kDa Plasmodium falciparum protein
Buffer: 100 mM Na-phosphate buffer, 400 mM NaCl, pH: 7.4
Experiment: SAXS data collected at Xenocs Xeuss 2.0 with MetalJet, Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University on 2019 Jul 3
A fragment-based approach identifies an allosteric pocket that impacts malate dehydrogenase activity Communications Biology 4(1) (2021)
Reyes Romero A, Lunev S, Popowicz G, Calderone V, Gentili M, Sattler M, Plewka J, Taube M, Kozak M, Holak T, Dömling A, Groves M
RgGuinier 3.6 nm
Dmax 11.4 nm
VolumePorod 223 nm3

SASDKA6 – Flavonoid-responsive regulator A (FrrA)

TetR/AcrR family transcriptional regulator experimental SAS data
CORAL model
Sample: TetR/AcrR family transcriptional regulator dimer, 48 kDa Bradyrhizobium diazoefficiens protein
Buffer: 20 mM Na2HPO4, 50 mM NaCl, 50 mM imidazole, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Sep 23
The Induction Mechanism of the Flavonoid-Responsive Regulator FrrA. FEBS J (2021)
Werner N, Werten S, Hoppen J, Palm GJ, Göttfert M, Hinrichs W
RgGuinier 3.4 nm
Dmax 9.0 nm
VolumePorod 93 nm3

SASDKB6 – Flavonoid-responsive regulator A (FrrA) in the presence of genistein

TetR/AcrR family transcriptional regulator5,7-dihydroxy-3-(4-hydroxyphenyl)chromen-4-one experimental SAS data
TetR/AcrR family transcriptional regulator 5,7-dihydroxy-3-(4-hydroxyphenyl)chromen-4-one Kratky plot
Sample: TetR/AcrR family transcriptional regulator dimer, 48 kDa Bradyrhizobium diazoefficiens protein
5,7-dihydroxy-3-(4-hydroxyphenyl)chromen-4-one monomer, 0 kDa
Buffer: 20 mM Na2HPO4, 50 mM NaCl, 50 mM imidazole, 0.08 mM genistein, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2015 Oct 27
The Induction Mechanism of the Flavonoid-Responsive Regulator FrrA. FEBS J (2021)
Werner N, Werten S, Hoppen J, Palm GJ, Göttfert M, Hinrichs W
RgGuinier 3.4 nm
Dmax 8.7 nm
VolumePorod 96 nm3

SASDKC6 – Flavonoid-responsive regulator A (FrrA) in the presence of naringenin

TetR/AcrR family transcriptional regulator5,7-dihydroxy-2-(4-hydroxyphenyl)chroman-4-one experimental SAS data
TetR/AcrR family transcriptional regulator 5,7-dihydroxy-2-(4-hydroxyphenyl)chroman-4-one Kratky plot
Sample: TetR/AcrR family transcriptional regulator dimer, 48 kDa Bradyrhizobium diazoefficiens protein
5,7-dihydroxy-2-(4-hydroxyphenyl)chroman-4-one monomer, 0 kDa
Buffer: 20 mM Na2HPO4, 50 mM NaCl, 50 mM imidazole, 1 mM naringenin, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Sep 23
The Induction Mechanism of the Flavonoid-Responsive Regulator FrrA. FEBS J (2021)
Werner N, Werten S, Hoppen J, Palm GJ, Göttfert M, Hinrichs W
RgGuinier 3.2 nm
Dmax 8.6 nm
VolumePorod 91 nm3

SASDL26 – CBD12 of CALX1.1 (apo state)

AT07459p experimental SAS data
CBD12 of CALX1.1 (apo state) Rg histogram
Sample: AT07459p monomer, 30 kDa Drosophila melanogaster protein
Buffer: 20 mM Tris, 5 mM β-mercaptoethanol, 200 mM NaCl, 1% v/v glycerol, pH: 7.4
Experiment: SAXS data collected at Xenocs Xeuss, Institute of Physics, University of São Paulo on 2018 Mar 8
Molecular insights on CALX-CBD12 inter-domain dynamics from MD simulations, RDCs and SAXS. Biophys J (2021)
de Souza Degenhardt MF, Vitale PAM, Abiko LA, Zacharias M, Sattler M, Oliveira CLP, Salinas RK
RgGuinier 2.5 nm
Dmax 8.7 nm
VolumePorod 41 nm3

SASDL36 – CBD12 of CALX1.1 in the calcium-bound state

AT07459p experimental SAS data
CBD12 of CALX1.1 in the calcium-bound state Rg histogram
Sample: AT07459p monomer, 30 kDa Drosophila melanogaster protein
Buffer: 20 mM Tris, 5 mM β-mercaptoethanol, 200 mM NaCl, 1% v/v glycerol, 0.8 mM CaCl2, pH: 7.4
Experiment: SAXS data collected at Xenocs Xeuss, Institute of Physics, University of São Paulo on 2018 Apr 13
Molecular insights on CALX-CBD12 inter-domain dynamics from MD simulations, RDCs and SAXS. Biophys J (2021)
de Souza Degenhardt MF, Vitale PAM, Abiko LA, Zacharias M, Sattler M, Oliveira CLP, Salinas RK
RgGuinier 2.7 nm
Dmax 9.3 nm
VolumePorod 40 nm3