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20 hits found for Molodenskiy

SASDLJ3 – SH3 and multiple ankyrin repeat domains protein 3 (wild type)

SH3 and multiple ankyrin repeat domains protein 3 experimental SAS data
CORAL model
Sample: SH3 and multiple ankyrin repeat domains protein 3 monomer, 88 kDa Rattus norvegicus protein
Buffer: 100mM NaH2PO4, 100mM NaCl, 0.5mM DTT,, pH: 6.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Jun 3
Autism associated SHANK3 missense point mutations impact conformational fluctuations and protein turnover at synapses. Elife 10 (2021)
...Molodenskiy D, Nia FH, Kreienkamp HJ, Svergun D, Kim E, Kostyukova AS, Kreutz MR, Mikhaylova M
RgGuinier 4.1 nm
Dmax 14.0 nm
VolumePorod 170 nm3

SASDLK3 – SH3 and multiple ankyrin repeat domains protein 3 with a point mutation (L68P)

SH3 and multiple ankyrin repeat domains protein 3 experimental SAS data
CORAL model
Sample: SH3 and multiple ankyrin repeat domains protein 3 monomer, 88 kDa Rattus norvegicus protein
Buffer: 100mM NaH2PO4, 100mM NaCl, 0.5mM DTT,, pH: 6.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Jun 3
Autism associated SHANK3 missense point mutations impact conformational fluctuations and protein turnover at synapses. Elife 10 (2021)
...Molodenskiy D, Nia FH, Kreienkamp HJ, Svergun D, Kim E, Kostyukova AS, Kreutz MR, Mikhaylova M
RgGuinier 4.1 nm
Dmax 14.8 nm
VolumePorod 224 nm3

SASDLL3 – SH3 and multiple ankyrin repeat domains protein 3 with a point mutation (R12C)

SH3 and multiple ankyrin repeat domains protein 3 experimental SAS data
CORAL model
Sample: SH3 and multiple ankyrin repeat domains protein 3 monomer, 87 kDa Rattus norvegicus protein
Buffer: 100mM NaH2PO4, 100mM NaCl, 0.5mM DTT,, pH: 6.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Jun 3
Autism associated SHANK3 missense point mutations impact conformational fluctuations and protein turnover at synapses. Elife 10 (2021)
...Molodenskiy D, Nia FH, Kreienkamp HJ, Svergun D, Kim E, Kostyukova AS, Kreutz MR, Mikhaylova M
RgGuinier 4.1 nm
Dmax 13.8 nm
VolumePorod 175 nm3

SASDMV3 – Sigma-Aldrich polystyrene nanospheres with a diameter of 100 nm

Nominal 100 nm diameter polystyrene spheres experimental SAS data
Nominal 100 nm diameter polystyrene spheres Kratky plot
Sample: Nominal 100 nm diameter polystyrene spheres monomer, 315312 kDa
Buffer: Water, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Apr 1
Standard polystyrene nanospheres (concentration series data)
Dima Molodenskiy
RgGuinier 33.0 nm
Dmax 100.0 nm
VolumePorod 520 nm3

SASDMW3 – Thermo Fisher polystyrene nanospheres with a diameter of 20 nm

Nominal 20 nm diameter polystyrene spheres experimental SAS data
Nominal 20 nm diameter polystyrene spheres Kratky plot
Sample: Nominal 20 nm diameter polystyrene spheres 0, 8 kDa
Buffer: Water, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Apr 1
Standard polystyrene nanospheres (concentration series data)
Dima Molodenskiy
RgGuinier 8.5 nm
Dmax 25.0 nm
VolumePorod 3 nm3

SASDKK4 – A-type ATP synthase

n-Dodecyl-β-D-MaltopyranosideA-type ATP synthaseMonoclonal Antibody Fragment experimental SAS data
OTHER model
Sample: n-Dodecyl-β-D-Maltopyranoside , 77 kDa synthetic construct
A-type ATP synthase monomer, 655 kDa Thermus thermophilus protein
Monoclonal Antibody Fragment dimer, 33 kDa Homo sapiens protein
Buffer: 20 mM Tris/HCl, 100 mM sucrose, 100 mM NaCl, 2 mM MgCl2, 10% glycerol, 0.05% b-DDM, pH: 8
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2013 Mar 3
MPBuilder: A PyMOL Plugin for Building and Refinement of Solubilized Membrane Proteins Against Small Angle X-ray Scattering Data Journal of Molecular Biology :166888 (2021)
Molodenskiy D, Svergun D, Mertens H
RgGuinier 8.0 nm
Dmax 27.0 nm
VolumePorod 1549 nm3

SASDK36 – LC-18t - ssDNA aptamer specific to lung adenocarcinoma cancer cells

Lung adenocarcinoma aptamer, truncated version experimental SAS data
GROMACS model
Sample: Lung adenocarcinoma aptamer, truncated version monomer, 11 kDa Artificially synthesized DNA
Buffer: Phosphate-buffered saline, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Oct 28
The Role of Small-Angle X-Ray Scattering and Molecular Simulations in 3D Structure Elucidation of a DNA Aptamer Against Lung Cancer Molecular Therapy - Nucleic Acids (2021)
...Molodenskiy D, Zabluda V, Veprintsev D, Sokolov A, Zukov R, Berezovski M, Tomilin F, Fedorov D, Alexeev Y, Kichkailo A
RgGuinier 2.1 nm
Dmax 6.7 nm
VolumePorod 16 nm3

SASDN77 – Truncated histone shaperone protein SET/TAF-Ib DC

SET nuclear proto-oncogene experimental SAS data
AMBER model
Sample: SET nuclear proto-oncogene dimer, 53 kDa Homo sapiens protein
Buffer: Sodium phosphate buffer, pH: 6.3
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Nov 11
PP2A is activated by cytochrome c upon formation of a diffuse encounter complex with SET/TAF-Iβ Computational and Structural Biotechnology Journal (2022)
...Molodenskiy D, Díaz-Quintana A, Martinho M, Gerbaud G, González-Arzola K, Velázquez-Campoy A, Svergun D, Belle V, De la Rosa M, Díaz-Moreno I
RgGuinier 3.1 nm
Dmax 9.7 nm
VolumePorod 87 nm3

SASDN87 – Mixture 1:2 of truncated histone shaperone protein SET/TAF-Ib DC with cytochrome c

Cytochrome cSET nuclear proto-oncogene experimental SAS data
SASREF model
Sample: Cytochrome c dimer, 24 kDa Homo sapiens protein
SET nuclear proto-oncogene dimer, 53 kDa Homo sapiens protein
Buffer: Sodium phosphate buffer, pH: 6.3
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Nov 11
PP2A is activated by cytochrome c upon formation of a diffuse encounter complex with SET/TAF-Iβ Computational and Structural Biotechnology Journal (2022)
...Molodenskiy D, Díaz-Quintana A, Martinho M, Gerbaud G, González-Arzola K, Velázquez-Campoy A, Svergun D, Belle V, De la Rosa M, Díaz-Moreno I
RgGuinier 4.2 nm
Dmax 16.0 nm

SASDED8 – Poly-L-Glutamic Acid in Dimethyl Sulfoxide (DMSO)

Poly-L-Glutamic Acid experimental SAS data
PYMOL model
Sample: Poly-L-Glutamic Acid , 6 kDa
Buffer: Dimethyl Sulfoxide (DMSO), pH:
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Dec 11
β2-Type Amyloidlike Fibrils of Poly-l-glutamic Acid Convert into Long, Highly Ordered Helices upon Dissolution in Dimethyl Sulfoxide. J Phys Chem B 122(50):11895-11905 (2018)
...Molodenskiy D, Wielgus-Kutrowska B, Johannessen C, Hernik-Magoń A, Tobias F, Bzowska A, Ścibisz G, Keiderling TA, Svergun D, Dzwolak W
RgGuinier 1.8 nm
Dmax 7.8 nm
VolumePorod 5 nm3

SASDJE6 – Metallothionein (MT) 2 protein from the plant Cicer arietinum

Metallothionein-like protein 2 experimental SAS data
Metallothionein (MT) 2 protein from the plant Cicer arietinum Rg histogram
Sample: Metallothionein-like protein 2 monomer, 8 kDa Cicer arietinum protein
Buffer: 10 mM Tris, 50 mM NaCl, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Aug 8
Structural Characterization of Plant Metallothionein
Dima Molodenskiy
RgGuinier 1.9 nm
Dmax 7.3 nm
VolumePorod 5 nm3

SASDFP8 – Carbonic anhydrase 2 from bovine erythrocytes - SEC-SAXS coupled to multiangle laser and quasi-elastic light scattering (MALLS and QELS)

Carbonic anhydrase 2 experimental SAS data
DAMMIN model
Sample: Carbonic anhydrase 2 monomer, 29 kDa Bos taurus protein
Buffer: 50 mM HEPES, 150 mM NaCl, 2% v/v glycerol, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Apr 5
Adding Size Exclusion Chromatography (SEC) and Light Scattering (LS) Devices to Obtain High-Quality Small Angle X-Ray Scattering (SAXS) Data Crystals 10(11):975 (2020)
...Molodenskiy D, Blanchet C, Svergun D, Jeffries C
RgGuinier 1.8 nm
Dmax 5.1 nm
VolumePorod 37 nm3

SASDJF6 – Apo-full-length protein titrated with Cd(II) ions

Metallothionein-like protein 2 experimental SAS data
Apo-full-length protein titrated with Cd(II) ions Rg histogram
Sample: Metallothionein-like protein 2 monomer, 8 kDa Cicer arietinum protein
Buffer: 10 mM Tris, 50 mM NaCl + 1mM TCEP (apoMT), pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Aug 8
Structural Characterization of Plant Metallothionein
Dima Molodenskiy
RgGuinier 2.6 nm
Dmax 10.0 nm
VolumePorod 13 nm3

SASDFQ8 – Bovine serum albumin, purified monomer - SEC-SAXS coupled to multiangle laser and quasi-elastic light scattering (MALLS and QELS)

Bovine serum albumin experimental SAS data
GASBOR model
Sample: Bovine serum albumin monomer, 66 kDa Bos taurus protein
Buffer: 50 mM HEPES, 150 mM NaCl, 2% v/v glycerol, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Apr 5
Adding Size Exclusion Chromatography (SEC) and Light Scattering (LS) Devices to Obtain High-Quality Small Angle X-Ray Scattering (SAXS) Data Crystals 10(11):975 (2020)
...Molodenskiy D, Blanchet C, Svergun D, Jeffries C
RgGuinier 2.8 nm
Dmax 8.0 nm
VolumePorod 98 nm3

SASDJG6 – The separated apo-linker region peptide

The separated apo-linker region peptide from the plant Cicer arietinum experimental SAS data
The separated apo-linker region peptide Rg histogram
Sample: The separated apo-linker region peptide from the plant Cicer arietinum monomer, 4 kDa Cicer arietinum protein
Buffer: 10 mM Tris, 50 mM NaCl, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Aug 8
Structural Characterization of Plant Metallothionein
Dima Molodenskiy
RgGuinier 1.4 nm
Dmax 6.5 nm
VolumePorod 1 nm3

SASDFR8 – Bovine serum albumin, purified dimer - SEC-SAXS coupled to multiangle laser and quasi-elastic light scattering (MALLS and QELS)

Bovine serum albumin experimental SAS data
GASBOR model
Sample: Bovine serum albumin dimer, 133 kDa Bos taurus protein
Buffer: 50 mM HEPES, 150 mM NaCl, 2% v/v glycerol, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Apr 5
Adding Size Exclusion Chromatography (SEC) and Light Scattering (LS) Devices to Obtain High-Quality Small Angle X-Ray Scattering (SAXS) Data Crystals 10(11):975 (2020)
...Molodenskiy D, Blanchet C, Svergun D, Jeffries C
RgGuinier 4.0 nm
Dmax 13.2 nm
VolumePorod 211 nm3

SASDJH6 – The CxxC-linker-CxxC construct binding 1 Cd(II) ion in a CdCys4 site

A CxxC-linker-CxxC construct binding 1 Cd(II) ion in a CdCys4 site experimental SAS data
The CxxC-linker-CxxC construct binding 1 Cd(II) ion in a CdCys4 site Rg histogram
Sample: A CxxC-linker-CxxC construct binding 1 Cd(II) ion in a CdCys4 site monomer, 5 kDa Cicer arietinum protein
Buffer: 10 mM Tris, 50 mM NaCl, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Aug 8
Structural Characterization of Plant Metallothionein
Dima Molodenskiy
RgGuinier 1.9 nm
Dmax 6.3 nm

SASDFS8 – Yeast alcohol dehydrogenase 1 - SEC-SAXS coupled to multiangle laser and quasi-elastic light scattering (MALLS and QELS)

Alcohol dehydrogenase 1 experimental SAS data
DAMMIN model
Sample: Alcohol dehydrogenase 1 tetramer, 147 kDa Saccharomyces cerevisiae protein
Buffer: 50 mM HEPES, 150 mM NaCl, 2% v/v glycerol, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Apr 5
Adding Size Exclusion Chromatography (SEC) and Light Scattering (LS) Devices to Obtain High-Quality Small Angle X-Ray Scattering (SAXS) Data Crystals 10(11):975 (2020)
...Molodenskiy D, Blanchet C, Svergun D, Jeffries C
RgGuinier 3.3 nm
Dmax 9.3 nm
VolumePorod 201 nm3

SASDFN8 – Apoferritin from horse spleen - SEC-SAXS coupled to multiangle laser and quasi-elastic light scattering (MALLS and QELS)

Apoferritin light chain experimental SAS data
DAMMIN model
Sample: Apoferritin light chain 24-mer, 479 kDa Equus caballus protein
Buffer: 50 mM HEPES, 150 mM NaCl, 2% v/v glycerol, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Apr 5
Adding Size Exclusion Chromatography (SEC) and Light Scattering (LS) Devices to Obtain High-Quality Small Angle X-Ray Scattering (SAXS) Data Crystals 10(11):975 (2020)
...Molodenskiy D, Blanchet C, Svergun D, Jeffries C
RgGuinier 5.4 nm
Dmax 12.5 nm
VolumePorod 679 nm3

SASDF99 – Bovine serum albumin monomer - SEC-SAXS/WAXS coupled to multiangle laser and quasi-elastic light scattering (MALLS and QELS)

Bovine serum albumin experimental SAS data
GASBOR model
Sample: Bovine serum albumin monomer, 66 kDa Bos taurus protein
Buffer: 50 mM HEPES, 3% v/v glycerol,, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Apr 23
Adding Size Exclusion Chromatography (SEC) and Light Scattering (LS) Devices to Obtain High-Quality Small Angle X-Ray Scattering (SAXS) Data Crystals 10(11):975 (2020)
...Molodenskiy D, Blanchet C, Svergun D, Jeffries C
RgGuinier 2.8 nm
Dmax 8.3 nm
VolumePorod 95 nm3