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SASDWJ7 – Wild type ferric binding protein (FbpA) in apo (no Fe) form in high ionic strength (HIS) buffer (PBS)

Iron-utilization periplasmic protein experimental SAS data
DAMFILT model
Sample: Iron-utilization periplasmic protein monomer, 34 kDa Haemophilus influenzae protein
Buffer: 10 mM Na2HPO4 . 7H2O 1.8 mM KH2PO4 137 mM NaCl 2.7 mM KCl 5% v/v Glycerol, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Dec 9
Conformational multiplicity of bacterial ferric binding protein revealed by small angle x-ray scattering and molecular dynamics calculations The Journal of Chemical Physics 158(8) (2023)
Liu G, Ekmen E, Jalalypour F, Mertens H, Jeffries C, Svergun D, Atilgan A, Atilgan C, Sayers Z
RgGuinier 2.1 nm
Dmax 6.5 nm
VolumePorod 39 nm3

SASDWK7 – D52A mutant of ferric binding protein (FbpA) in holo (with Fe) form in high ionic strength (HIS) buffer (PBS)

Iron-utilization periplasmic protein experimental SAS data
DAMMIN model
Sample: Iron-utilization periplasmic protein monomer, 34 kDa Haemophilus influenzae protein
Buffer: 10 mM Na2HPO4 . 7H2O 1.8 mM KH2PO4 137 mM NaCl 2.7 mM KCl 5% v/v Glycerol, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Dec 9
Conformational multiplicity of bacterial ferric binding protein revealed by small angle x-ray scattering and molecular dynamics calculations The Journal of Chemical Physics 158(8) (2023)
Liu G, Ekmen E, Jalalypour F, Mertens H, Jeffries C, Svergun D, Atilgan A, Atilgan C, Sayers Z
RgGuinier 2.0 nm
Dmax 5.9 nm
VolumePorod 33 nm3

SASDWL7 – D52A mutant of ferric binding protein (FbpA) in apo (no Fe) form in high ionic strength (HIS) buffer (PBS)

Iron-utilization periplasmic protein experimental SAS data
DAMMIN model
Sample: Iron-utilization periplasmic protein monomer, 34 kDa Haemophilus influenzae protein
Buffer: 10 mM Na2HPO4 . 7H2O 1.8 mM KH2PO4 137 mM NaCl 2.7 mM KCl 5% v/v Glycerol, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Sep 19
Conformational multiplicity of bacterial ferric binding protein revealed by small angle x-ray scattering and molecular dynamics calculations The Journal of Chemical Physics 158(8) (2023)
Liu G, Ekmen E, Jalalypour F, Mertens H, Jeffries C, Svergun D, Atilgan A, Atilgan C, Sayers Z
RgGuinier 2.1 nm
Dmax 6.2 nm
VolumePorod 40 nm3

SASDWM7 – D52A mutant of ferric binding protein (FbpA) in holo (with Fe) form in low ionic strength (LIS) buffer (1/10 PBS)

Iron-utilization periplasmic protein experimental SAS data
DAMFILT model
Sample: Iron-utilization periplasmic protein monomer, 34 kDa Haemophilus influenzae protein
Buffer: 1 mM Na2HPO4.7H2O, 0.18 mM KH2PO4, 13.7 mM NaCl, 0.27 mM KCl, 5%v/v Glycerol, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Aug 20
Conformational multiplicity of bacterial ferric binding protein revealed by small angle x-ray scattering and molecular dynamics calculations The Journal of Chemical Physics 158(8) (2023)
Liu G, Ekmen E, Jalalypour F, Mertens H, Jeffries C, Svergun D, Atilgan A, Atilgan C, Sayers Z
RgGuinier 2.0 nm
Dmax 6.1 nm
VolumePorod 24 nm3

SASDWN7 – Wild type ferric binding protein (FbpA) in apo (no Fe) form in low ionic strength (LIS) buffer (1/10 PBS)

Iron-utilization periplasmic protein experimental SAS data
DAMFILT model
Sample: Iron-utilization periplasmic protein monomer, 34 kDa Haemophilus influenzae protein
Buffer: 1 mM Na2HPO4.7H2O, 0.18 mM KH2PO4, 13.7 mM NaCl, 0.27 mM KCl, 5%v/v Glycerol, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Aug 20
Conformational multiplicity of bacterial ferric binding protein revealed by small angle x-ray scattering and molecular dynamics calculations The Journal of Chemical Physics 158(8) (2023)
Liu G, Ekmen E, Jalalypour F, Mertens H, Jeffries C, Svergun D, Atilgan A, Atilgan C, Sayers Z
RgGuinier 2.1 nm
Dmax 6.3 nm
VolumePorod 35 nm3

SASDWP7 – Wild type ferric binding protein (FbpA) in holo (with Fe) form in low ionic strength (LIS) buffer (1/10 PBS)

Iron-utilization periplasmic protein experimental SAS data
DAMMIN model
Sample: Iron-utilization periplasmic protein monomer, 34 kDa Haemophilus influenzae protein
Buffer: 1 mM Na2HPO4.7H2O, 0.18 mM KH2PO4, 13.7 mM NaCl, 0.27 mM KCl, 5%v/v Glycerol, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Aug 20
Conformational multiplicity of bacterial ferric binding protein revealed by small angle x-ray scattering and molecular dynamics calculations The Journal of Chemical Physics 158(8) (2023)
Liu G, Ekmen E, Jalalypour F, Mertens H, Jeffries C, Svergun D, Atilgan A, Atilgan C, Sayers Z
RgGuinier 2.0 nm
Dmax 6.1 nm
VolumePorod 29 nm3

SASDPJ3 – IMP-1 saRNA encoding NSP1-4 of VEEV and the spike glycoprotein of SARS-CoV-2

IMP-1 saRNA experimental SAS data
IMP-1 saRNA Kratky plot
Sample: IMP-1 saRNA monomer, 3720 kDa RNA
Buffer: 5 mM Sodium Citrate, pH: 6.4
Experiment: SAXS data collected at B21, Diamond Light Source on 2021 Apr 27
Biophysical characterisation of the structure of a SARS-CoV-2 self-amplifying—RNA (saRNA) vaccine Biology Methods and Protocols (2023)
Myatt D, Wharram L, Graham C, Liddell J, Branton H, Pizzey C, Cowieson N, Rambo R, Shattock R
RgGuinier 23.8 nm
Dmax 85.9 nm
VolumePorod 6265 nm3

SASDD73 – Flavin reductase Pden_5119

NADPH-dependent FMN reductase experimental SAS data
SWISSMODEL model
Sample: NADPH-dependent FMN reductase dimer, 41 kDa Paracoccus denitrificans protein
Buffer: 50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole, pH: 8
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2016 Feb 22
Structural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans. Int J Mol Sci 24(4) (2023)
Kryl M, Sedláček V, Kučera I
RgGuinier 2.3 nm
Dmax 6.3 nm
VolumePorod 70 nm3

SASDKD6 – NURS complex subunit red1

NURS complex subunit red1 experimental SAS data
NURS complex subunit red1 Kratky plot
Sample: NURS complex subunit red1 monomer, 8 kDa Schizosaccharomyces pombe (strain … protein
Buffer: 20 mM HEPES, pH 7.5, 150 mM NaCl, 1mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Nov 12
Mechanistic insights into RNA surveillance by the canonical poly(A) polymerase Pla1 of the MTREC complex. Nat Commun 14(1):772 (2023)
Soni K, Sivadas A, Horvath A, Dobrev N, Hayashi R, Kiss L, Simon B, Wild K, Sinning I, Fischer T
RgGuinier 2.5 nm
Dmax 8.7 nm
VolumePorod 12 nm3

SASDKE6 – Poly(A) polymerase pla1 bound to the NURS complex subunit red1

NURS complex subunit red1Poly(A) polymerase pla1 experimental SAS data
CORAL model
Sample: NURS complex subunit red1 monomer, 8 kDa Schizosaccharomyces pombe (strain … protein
Poly(A) polymerase pla1 monomer, 65 kDa Schizosaccharomyces pombe (strain … protein
Buffer: 20 mM HEPES, pH 7.5, 150 mM NaCl, 1mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Nov 12
Mechanistic insights into RNA surveillance by the canonical poly(A) polymerase Pla1 of the MTREC complex. Nat Commun 14(1):772 (2023)
Soni K, Sivadas A, Horvath A, Dobrev N, Hayashi R, Kiss L, Simon B, Wild K, Sinning I, Fischer T
RgGuinier 3.3 nm
Dmax 10.7 nm
VolumePorod 138 nm3