Browse by MODEL: Ab initio only

SASDKM9 – Lymphostatin pH5.5

Efa1/LifA protein experimental SAS data
DAMFILT model
Sample: Efa1/LifA protein monomer, 367 kDa Escherichia coli O127:H6 … protein
Buffer: 50 mM Bis-Tris, 100 mM NaCl, 3 % (v/v) glycerol, pH: 5.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Jun 29
Activity of lymphostatin, a lymphocyte inhibitory virulence factor of pathogenic Escherichia coli, is dependent on a cysteine protease motif. J Mol Biol :167200 (2021)
Bease AG, Blackburn EA, Chintoan-Uta C, Webb S, Cassady-Cain RL, Stevens MP
RgGuinier 5.9 nm
Dmax 19.7 nm
VolumePorod 565 nm3

SASDKN9 – Lymphostatin C1480A mutant pH 7.5

Efa1/LifA protein (C1480A mutant) experimental SAS data
DAMMIF model
Sample: Efa1/LifA protein (C1480A mutant) monomer, 367 kDa Escherichia coli O127:H6 … protein
Buffer: 50 mM Bis-Tris, 100 mM NaCl, 3 % (v/v) glycerol, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Jun 29
Activity of lymphostatin, a lymphocyte inhibitory virulence factor of pathogenic Escherichia coli, is dependent on a cysteine protease motif. J Mol Biol :167200 (2021)
Bease AG, Blackburn EA, Chintoan-Uta C, Webb S, Cassady-Cain RL, Stevens MP
RgGuinier 5.9 nm
Dmax 19.1 nm
VolumePorod 557 nm3

SASDKP9 – Lymphostatin C1480A mutant pH5.5

Efa1/LifA protein (C1480A mutant) experimental SAS data
DAMFILT model
Sample: Efa1/LifA protein (C1480A mutant) monomer, 367 kDa Escherichia coli O127:H6 … protein
Buffer: 50 mM Bis-Tris, 100 mM NaCl, 3 % (v/v) glycerol, pH: 5.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Jun 29
Activity of lymphostatin, a lymphocyte inhibitory virulence factor of pathogenic Escherichia coli, is dependent on a cysteine protease motif. J Mol Biol :167200 (2021)
Bease AG, Blackburn EA, Chintoan-Uta C, Webb S, Cassady-Cain RL, Stevens MP
RgGuinier 5.8 nm
Dmax 19.3 nm
VolumePorod 560 nm3

SASDMM2 – Thalassiosira pseudonana iota Carbonic anhydrase (ι-CA)

iota carbonic anhydrase experimental SAS data
DAMMIF model
Sample: Iota carbonic anhydrase tetramer, 260 kDa Thalassiosira pseudonana protein
Buffer: 20 mM Tris, 150 mM NaCl, pH: 8
Experiment: SAXS data collected at SWING, SOLEIL on 2019 Mar 28
Structural Contour Map of the Iota Carbonic Anhydrase from the Diatom Thalassiosira pseudonana Using a Multiprong Approach. Int J Mol Sci 22(16) (2021)
Jensen EL, Receveur-Brechot V, Hachemane M, Wils L, Barbier P, Parsiegla G, Gontero B, Launay H
RgGuinier 6.7 nm
Dmax 25.0 nm
VolumePorod 500 nm3

SASDMY3 – Lysozyme amyloid fibril (LAF)

lysozyme amyloid fibril experimental SAS data
DAMMIF model
Sample: Lysozyme amyloid fibril, 1 kDa Gallus gallus protein
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 38.4 nm
Dmax 80.0 nm

SASDM44 – LAF + P10 nanocomposite (NP added before fibrilization)

lysozyme amyloid fibrilFe3O4 nanoparticles; nominal diameter 10 nm (hydrodynamic diameter) experimental SAS data
DAMMIN model
Sample: Lysozyme amyloid fibril, 1 kDa Gallus gallus protein
Fe3O4 nanoparticles; nominal diameter 10 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 22.3 nm
Dmax 70.0 nm

SASDM54 – LAF + P30 nanocomposite (NP added before fibrilization)

lysozyme amyloid fibrilFe3O4 nanoparticles; nominal diameter 30 nm (hydrodynamic diameter) experimental SAS data
DAMMIN model
Sample: Lysozyme amyloid fibril, 1 kDa Gallus gallus protein
Fe3O4 nanoparticles; nominal diameter 30 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 22.5 nm
Dmax 95.0 nm

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

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