Browse by ORGANISM: other species

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

SASDQG7 – Thermoanearobacter tengcongensis (Tte) fecB RNA riboswitch aptamer domain (rCbl)

Thermoanearobacter tengcongensis (Tte) fecB riboswitch aptamer domain experimental SAS data
OTHER model
Sample: Thermoanearobacter tengcongensis (Tte) fecB riboswitch aptamer domain, 68 kDa marine metagenome RNA
Buffer: 50 mM MES pH 6.0, 10 mM KCl, 1 mM MgCl2, pH: 6
Experiment: SAXS data collected at 12-ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Apr 18
Visualizing RNA conformational and architectural heterogeneity in solution. Nat Commun 14(1):714 (2023)
Ding J, Lee YT, Bhandari Y, Schwieters CD, Fan L, Yu P, Tarosov SG, Stagno JR, Ma B, Nussinov R, Rein A, Zhang J, Wang YX
RgGuinier 5.9 nm
Dmax 20.7 nm
VolumePorod 206 nm3

SASDQH7 – Thermoanearobacter tengcongensis (Tte) fecB RNA riboswitch aptamer domain (rCbl) in the presence of coenzyme B12

Thermoanearobacter tengcongensis (Tte) fecB riboswitch aptamer domain experimental SAS data
OTHER model
Sample: Thermoanearobacter tengcongensis (Tte) fecB riboswitch aptamer domain, 68 kDa marine metagenome RNA
Buffer: 50 mM MES pH 6.0, 10 mM KCl, 1 mM MgCl2, 4-18 μM coenzyme B12 ligand, pH: 6
Experiment: SAXS data collected at 12-ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Apr 18
Visualizing RNA conformational and architectural heterogeneity in solution. Nat Commun 14(1):714 (2023)
Ding J, Lee YT, Bhandari Y, Schwieters CD, Fan L, Yu P, Tarosov SG, Stagno JR, Ma B, Nussinov R, Rein A, Zhang J, Wang YX
RgGuinier 5.7 nm
Dmax 19.7 nm
VolumePorod 230 nm3