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SASDPN3 – Vibrio cholerae ParD2:ParE2 antitoxin:toxin complex

Antitoxin ParDToxin experimental SAS data
CUSTOM IN-HOUSE model
Sample: Antitoxin ParD hexamer, 54 kDa Vibrio cholerae serotype … protein
Toxin, 25 kDa Vibrio cholerae serotype … protein
Buffer: 20 mM Tris, 150 mM NaCl, 1 mM TCEP, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 Mar 6
Toxin:antitoxin ratio sensing autoregulation of the Vibrio cholerae parDE2 module. Sci Adv 10(1):eadj2403 (2024)
Garcia-Rodriguez G, Girardin Y, Kumar Singh R, Volkov AN, Van Dyck J, Muruganandam G, Sobott F, Charlier D, Loris R
RgGuinier 3.0 nm
Dmax 11.0 nm
VolumePorod 140 nm3

SASDPE2 – Starch adherence system protein 6 (Sas6)

Dockerin type I repeat experimental SAS data
MULTIFOXS model
Sample: Dockerin type I repeat monomer, 69 kDa Ruminococcus bromii protein
Buffer: phosphate buffered saline, 1 mM TCEP, pH: 7
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Nov 14
The Ruminococcus bromii amylosome protein Sas6 binds single and double helical α-glucan structures in starch. Nat Struct Mol Biol (2024)
Photenhauer AL, Villafuerte-Vega RC, Cerqueira FM, Armbruster KM, Mareček F, Chen T, Wawrzak Z, Hopkins JB, Vander Kooi CW, Janeček Š, Ruotolo BT, Koropatkin NM
RgGuinier 3.0 nm
Dmax 9.0 nm
VolumePorod 97 nm3

SASDTG2 – LCP domain of LytR from Streptococcus dysgalactiae in the presence of geranylgeranyl diphosphate (150 mM NaCl)

Biofilm regulatory protein experimental SAS data
Biofilm regulatory protein Kratky plot
Sample: Biofilm regulatory protein monomer, 34 kDa Streptococcus dysgalactiae subsp. … protein
Buffer: 50 mM HEPES, 150 mM NaCl, 5 mM MgCl2, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2022 Jun 1
Structural insights of an LCP protein-LytR-from Streptococcus dysgalactiae subs. dysgalactiae through biophysical and in silico methods. Front Chem 12:1379914 (2024)
Paquete-Ferreira J, Freire F, Fernandes HS, Muthukumaran J, Ramos J, Bryton J, Panjkovich A, Svergun D, Santos MFA, Correia MAS, Fernandes AR, Romão MJ, Sousa SF, Santos-Silva T
RgGuinier 2.5 nm
Dmax 8.0 nm
VolumePorod 83 nm3

SASDTH2 – LCP domain of LytR from Streptococcus dysgalactiae in the absence of ligand (150 mM NaCl)

Biofilm regulatory protein experimental SAS data
Biofilm regulatory protein Kratky plot
Sample: Biofilm regulatory protein monomer, 34 kDa Streptococcus dysgalactiae subsp. … protein
Buffer: 50 mM HEPES, 150 mM NaCl, 5 mM MgCl2, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2022 Jun 1
Structural insights of an LCP protein-LytR-from Streptococcus dysgalactiae subs. dysgalactiae through biophysical and in silico methods. Front Chem 12:1379914 (2024)
Paquete-Ferreira J, Freire F, Fernandes HS, Muthukumaran J, Ramos J, Bryton J, Panjkovich A, Svergun D, Santos MFA, Correia MAS, Fernandes AR, Romão MJ, Sousa SF, Santos-Silva T
RgGuinier 2.4 nm
Dmax 9.0 nm
VolumePorod 76 nm3

SASDTU4 – 24×FerSUMO - Chimeric protein complex of ferritin from Helicobacter pylori fused to an N-terminal His6-SUMO protein tag

Bacterial non-heme ferritin (N19Q, I59V, N-terminal His-SUMO fusion) experimental SAS data
CORAL model
Sample: Bacterial non-heme ferritin (N19Q, I59V, N-terminal His-SUMO fusion) 24-mer, 755 kDa Helicobacter pylori (strain … protein
Buffer: 25 mM Tris, 150 mM NaCl, pH: 7.4
Experiment: SAXS data collected at Rigaku MicroMax 007-HF, Moscow Institute of Physics and Technology (MIPT) on 2022 Jul 30
Ferritin-based fusion protein shows octameric deadlock state of self-assembly Biochemical and Biophysical Research Communications 690:149276 (2024)
Sudarev V, Gette M, Bazhenov S, Tilinova O, Zinovev E, Manukhov I, Kuklin A, Ryzhykau Y, Vlasov A
RgGuinier 7.6 nm
Dmax 25.0 nm
VolumePorod 2010 nm3

SASDTV4 – 8×FerSUMO - Chimeric protein complex of ferritin from Helicobacter pylori fused to an N-terminal His6-SUMO protein tag

Bacterial non-heme ferritin (N19Q, I59V, N-terminal His-SUMO fusion) experimental SAS data
PHYRE2 model
Sample: Bacterial non-heme ferritin (N19Q, I59V, N-terminal His-SUMO fusion) octamer, 252 kDa Helicobacter pylori (strain … protein
Buffer: 25 mM Tris, 150 mM NaCl, pH: 7.4
Experiment: SAXS data collected at Rigaku MicroMax 007-HF, Moscow Institute of Physics and Technology (MIPT) on 2022 Jul 17
Ferritin-based fusion protein shows octameric deadlock state of self-assembly Biochemical and Biophysical Research Communications 690:149276 (2024)
Sudarev V, Gette M, Bazhenov S, Tilinova O, Zinovev E, Manukhov I, Kuklin A, Ryzhykau Y, Vlasov A
RgGuinier 5.4 nm
Dmax 16.0 nm
VolumePorod 618 nm3

SASDTW4 – Ferritin from Helicobacter pylori with an N-terminal His6-tag

Bacterial non-heme ferritin (N19Q, I59V) experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Bacterial non-heme ferritin (N19Q, I59V) 24-mer, 480 kDa Helicobacter pylori (strain … protein
Buffer: 20 mM Tris, pH: 8
Experiment: SAXS data collected at Rigaku MicroMax 007-HF, Moscow Institute of Physics and Technology (MIPT) on 2022 Dec 14
Ferritin-based fusion protein shows octameric deadlock state of self-assembly Biochemical and Biophysical Research Communications 690:149276 (2024)
Sudarev V, Gette M, Bazhenov S, Tilinova O, Zinovev E, Manukhov I, Kuklin A, Ryzhykau Y, Vlasov A
RgGuinier 5.6 nm
Dmax 14.5 nm
VolumePorod 674 nm3

SASDTK5 – Heme acquisition system protein A (39.9 kDa dimer from Pseudomonas protegens PF-5)

Heme acquisition protein HasAp experimental SAS data
DAMMIN model
Sample: Heme acquisition protein HasAp dimer, 38 kDa Pseudomonas fluorescens (strain … protein
Buffer: 50 mM CHES, 5 % glycerol, pH: 9.5
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2023 Feb 24
Heme-substituted protein assembly bridged by synthetic porphyrin: achieving controlled configuration while maintaining rotational freedom RSC Advances 14(13):8829-8836 (2024)
Inaba H, Shisaka Y, Ariyasu S, Sakakibara E, Ueda G, Aiba Y, Shimizu N, Sugimoto H, Shoji O
RgGuinier 2.8 nm
Dmax 9.1 nm
VolumePorod 54 nm3

SASDRR7 – Radical SAM enzyme peptide epimerase in the presence of SAM (S-adenosyl-L-methionine) and a peptide subtrate

Putative peptide biosynthesis protein YydG experimental SAS data
DADIMODO model
Sample: Putative peptide biosynthesis protein YydG dimer, 80 kDa Bacillus subtilis (strain … protein
Buffer: 25 mM HEPES, 150 mM NaCl, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at SWING, SOLEIL on 2022 Nov 30
Structural and mechanistic basis for RiPP epimerization by a radical SAM enzyme. Nat Chem Biol (2023)
Kubiak X, Polsinelli I, Chavas LMG, Fyfe CD, Guillot A, Fradale L, Brewee C, Grimaldi S, Gerbaud G, Thureau A, Legrand P, Berteau O, Benjdia A
RgGuinier 2.9 nm
Dmax 12.0 nm
VolumePorod 113 nm3

SASDRS7 – Radical SAM enzyme peptide epimerase in the presence of SAM (S-adenosyl-L-methionine)

Putative peptide biosynthesis protein YydG experimental SAS data
DADIMODO model
Sample: Putative peptide biosynthesis protein YydG dimer, 80 kDa Bacillus subtilis (strain … protein
Buffer: 25 mM HEPES, 150 mM NaCl, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at SWING, SOLEIL on 2022 Nov 29
Structural and mechanistic basis for RiPP epimerization by a radical SAM enzyme. Nat Chem Biol (2023)
Kubiak X, Polsinelli I, Chavas LMG, Fyfe CD, Guillot A, Fradale L, Brewee C, Grimaldi S, Gerbaud G, Thureau A, Legrand P, Berteau O, Benjdia A
RgGuinier 2.9 nm
Dmax 11.8 nm
VolumePorod 115 nm3