{"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":[]}