The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
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{
"code": "SASDUV2",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Novel lipid-interaction motifs within the C-terminal domain of Septin10 from Schistosoma mansoni",
"publication": {
"title": "Novel lipid-interaction motifs within the C-terminal domain of Septin10 from Schistosoma mansoni",
"author_list": "Cavini I, Fontes M, Zeraik A, Lopes J, Araújo A",
"journal": "Biochimica et Biophysica Acta (BBA) - Biomembranes",
"doi": "10.1016/j.bbamem.2024.184371",
"pmid": null,
"published_date": "2024 Jul"
},
"status": "released",
"submitted_date": "2024-02-08",
"released_date": "2024-07-17"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDUV2.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDUV2.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUV2_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUV2_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDUV2_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUV2_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDUV2.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Eiger 4M",
"resolution": 75.0
},
"name": "Diamond Light Source",
"city": "Didcot",
"country": "UK",
"beamline_name": "B21",
"beam_geometry": null,
"type_of_source": "X-ray synchrotron",
"point_source": null,
"line_collimation": null,
"sample_path_length": null,
"line_collimation_slitlength": null,
"line_collimation_integrationwidth": null,
"xray_energy": null,
"beam_profile_ah": null,
"beam_profile_al": null
},
"sample": {
"molecule": [
{
"long_name": "Septin-10",
"short_name": "MBP-SmSEPT10C",
"sequence": "MAHHHHHHSSGMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTSGSFRDDEKMSLQETYEKRRELQRKELQQKEEEMRQMFVQRVKEKEQVLKEAERELQTKFESLKKTHAEEKKKLEEKKRFLEEEIAAFERRKQLAEQARQGNLTMKKRK",
"organism": "Schistosoma mansoni",
"uniprot_code": "G4VFI8",
"uniprot_range_first": 307,
"uniprot_range_last": 412,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MTADVLKALPPDVRTLKLSGHVGFDSLPDQLVNKAISQGFVFNILCVGETGIGKSTLLET\nLFNQKFDFSPSNHDLTDPKLKAVTYDLKEANVKLKLTVVETCGYGDQINKENNIKPVVDY\nIDNQFENYLQEELKMKRSMQAFHDTRVHVCLYFIAPTGHSLKSIDLVAMKKLENKVNVIP\nVIAKSDTITKSELQKFKARILSEIQSNEIGIYQFPTDDEAVSETNSVMNQHIPFAVVGSS\nEEVKINGKTVRVRQYPWGSVQVENENHCDFVRLREMLLRVNMEDLRERTHGVHYETYRRQ\nRLIEMGFRDDEKMSLQETYEKRRELQRKELQQKEEEMRQMFVQRVKEKEQVLKEAERELQ\nTKFESLKKTHAEEKKKLEEKKRFLEEEIAAFERRKQLAEQARQGNLTMKKRK",
"mw": 55.025,
"total_mw": 110.05,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "Maltose binding protein (MBP)-fused Schistosoma mansoni Septin-10 C-terminal domain. A tripeptide linker (Ser-Gly-Ser) was used between the MBP (in the N-terminus of the protein fusion) and the coiled-coil sequence. The MBP also contains an additional N-terminal polyhistidine tag."
}
],
"buffer": {
"name": "50 mM Tris, 150 mM NaCl",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "MBP-fused Schistosoma mansoni Septin-10 C-terminal coiled-coil domain (MBP-SmSEPT10C)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": null,
"full_name": "University of Sao Paulo",
"webpage": null
}
],
"contributor_name": "Italo Augusto",
"contributor_surname": "Cavini",
"orcid": "https://orcid.org/0000-0003-2035-6584"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2023-05-17",
"storage_temperature": -0.1,
"cell_temperature": 15.0,
"exposure_time": 3.0,
"number_of_frames": 600,
"wavelength": 0.09464,
"sample_detector_distance": 3.7209,
"concentration_min": null,
"concentration_max": 5.0,
"sample_volume": 45.0,
"flow_rate": 0.08,
"s_min": 0.045,
"s_max": 3.4,
"total_exposure_time": null,
"seccolumn": 48
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDUV2_fit1_model1_img.png",
"software": "OmegaFold",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "OmegaFold",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDUV2_fit1_model1.pdb",
"model_mw": 110.0,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "Output model",
"user": 918
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDUV2_fit1_fitfoxs_img.png",
"software": "MultiFoXS",
"chi_square_value": 2.292588,
"p_value": 0.0,
"fit_residual_plot": "SASDUV2_fit1_fitfoxsresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDUV2_fit1.dat",
"fit_log": null,
"software_version": null,
"description": "Fitting of the scattering profile using a model based on a parallel coiled-coil prediction from OmegaFold. A flexible region of five residues in the linker between the MBP fusion and the coiled coil was used."
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDUV2_fit2_model1_img.png",
"software": "AlphaFold",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDUV2_fit2_model1.pdb",
"model_mw": 110.0,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "AF-multimer (antiparallel coiled coil)",
"user": 918
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDUV2_fit2_model2_img.png",
"software": "OmegaFold",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "OmegaFold",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDUV2_fit2_model2.pdb",
"model_mw": 110.0,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "OmegaFold (parallel)",
"user": 918
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDUV2_fit2_fitfoxs_img.png",
"software": "MultiFoXS",
"chi_square_value": 1.857145,
"p_value": 0.0,
"fit_residual_plot": "SASDUV2_fit2_fitfoxsresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDUV2_fit2.dat",
"fit_log": null,
"software_version": null,
"description": "Two-state ensemble using parallel+antiparallel solutions. Weights, 0.794:0.206 (P:AP)."
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDUV2_fit3_model1_img.png",
"software": "DAMMIN",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "dammin, ATSAS 3.2.1 (r14885)",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDUV2_fit3_model1.cif",
"model_mw": null,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/Sm10C.log",
"symmetry": null,
"comment": null,
"user": 918
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDUV2_fit3_fixed_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 1.287,
"p_value": 0.0014,
"fit_residual_plot": "SASDUV2_fit3_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDUV2_fit3.fir",
"fit_log": null,
"software_version": null,
"description": "Single DAMMIN run done on ATSAS online server. Symmetry, P1; Anisotropy assumptions, none; Mode, expert; dummy radius, 5 Angstroms."
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "The modelling presented are (from top to bottom): 1) MultiFoXS using parallel coiled-coil model; 2) MultiFoXS using parallel and antiparallel coiled-coil models (79:21 weight); 3) DAMMIN bead model (in P1 symmetry).",
"experiment_description": "Synchrotron SAXS data from solutions MBP-SmSEPT10C in 50 mM Tris, 150 mM NaCl, pH 7.5 were collected on the B21 beam line at the Diamond Light Source (Didcot, UK) using a Eiger 4M detector at a sample-detector distance of 3.7 m and at a wavelength of λ = 0.09464 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 45.00 μl sample at 5 mg/ml was injected at a 0.08 ml/min flow rate onto a GE Superdex 200 Increase 3.2/300 column at 15°C. 600 successive 3 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.",
"tags": [],
"intensity_unit": "1/cm",
"experimental_mw": 109.1,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 109.0,
"porod_mw_error": null,
"pddf_i0": 0.0339,
"pddf_i0_error": null,
"guinier_i0": 0.0322655,
"guinier_i0_error": null,
"pddf_rg": 6.74,
"pddf_rg_error": null,
"guinier_rg": 5.72,
"guinier_rg_error": 0.3,
"pddf_dmax": 27.4,
"pddf_dmax_error": null,
"porod_volume": 175.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 41,
"guinier_point_last": 126,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDUV2_datloglog_img.png",
"symmetry": null,
"last_modified": "2024-07-17T16:24:14.682629+02:00",
"bragg_peak": []
}
