{"code":"SASDVH9","status":"Published","type_of_curve":"Merged","angular_unit":"1/A","project":{"title":"Allergen-induced structural rearrangements in IgE: insights from SAXS and molecular dynamics.","publication":{"title":"Allergen-induced structural rearrangements in IgE: insights from SAXS and molecular dynamics.","author_list":"Gómez-Velasco H, García-Ramírez B, Siliqi D, Graewert MA, Quintero-Martinez A, Ortega E, Rodríguez-Romero A","journal":"Int J Biol Macromol","doi":"10.1016/j.ijbiomac.2025.147658","pmid":"40953619","published_date":"2025 Sep 13"},"status":"released","submitted_date":"2025-05-07","released_date":"2025-09-17"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDVH9.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDVH9.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVH9_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVH9_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVH9_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVH9_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDVH9.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":"Profilin-2","short_name":"PRF","sequence":"MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSDDDDKMSWQAYVDDHLMCEIEGNHLSAAAIIGQDGSVWAQSANFPQFKSEEITGIMSDFHEPGTLAPTGLYIGGTKYMVIQGEPGAVIRGKKGPGGVTVKKTNQALIIGIYDEPMTPGQCNMIVERLGDYLIDQGY","organism":"Hevea brasiliensis","uniprot_code":"Q9STB6","uniprot_range_first":1,"uniprot_range_last":131,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MSWQAYVDDHLMCEIEGNHLSAAAIIGQDGSVWAQSANFPQFKSEEITGIMSDFHEPGTL\nAPTGLYIGGTKYMVIQGEPGAVIRGKKGPGGVTVKKTNQALIIGIYDEPMTPGQCNMIVE\nRLGDYLIDQGY","mw":18.283,"total_mw":18.283,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":"Allergen Hev b 8 protein (profilin). The protein construct contains an additional 39 non-native amino acids at the N-terminus (MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSDDDDK)."}],"buffer":{"name":"20 mM Tris, 50 mM NaCl","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":8.4,"deuteration":null},"purity_method":null,"name":"allergen Hev b 8 protein, Profilin-2 (TAG)","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":null,"address":"Bari, Italy","full_name":"CNR - Institute of Crystallography, Bari, Italy","webpage":"http://www.ba.ic.cnr.it"}],"contributor_name":"Dritan","contributor_surname":"Siliqi","orcid":"https://orcid.org/0000-0003-1415-8725"}],"concentration_method":null,"concentration_unit":null,"date":"2024-10-03","storage_temperature":4.0,"cell_temperature":20.0,"exposure_time":1.0,"number_of_frames":20,"wavelength":0.094,"sample_detector_distance":3.7,"concentration_min":0.86,"concentration_max":6.9,"sample_volume":50.0,"flow_rate":0.06,"s_min":0.045,"s_max":3.4,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDVH9_fit1_model1_img.png","software":"CORAL","pdb_link":[{"pdb_code":"7sbd","ext_code":"7SBD","ext_type":"pdb","difference_with_model":"identical"}],"model_title":null,"type_of_model":"mix","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDVH9_fit1_model1.pdb","model_mw":15.06,"bead_radius":1.9,"log":"https://www.sasbdb.org/media/log_files/CORALonl_882.log","symmetry":"P1","comment":"Added the TAG by 40 dummy atoms . The model used is Chain C from 7sbd","user":396}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVH9_fit1_fixed_fit_img.png","software":"CORAL","chi_square_value":0.33,"p_value":0.0,"fit_residual_plot":"SASDVH9_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDVH9_fit1.fit","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/CORALonl_882.log","software_version":null,"description":""},{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDVH9_fit2_model1_img.png","software":"GASBOR","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":"3.2.1","model_data":"https://www.sasbdb.org/media/pdb_file/SASDVH9_fit2_model1.cif","model_mw":null,"bead_radius":null,"log":"https://www.sasbdb.org/media/log_files/GASBORon_2854.log","symmetry":"P1","comment":null,"user":396}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVH9_fit2_fixed_fit_img.png","software":"GASBOR","chi_square_value":0.17,"p_value":0.0007,"fit_residual_plot":"SASDVH9_fit2_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDVH9_fit2.fir","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/GASBORon_2854.log","software_version":"3.2.1","description":"GASBOR model shows an tail  , compatible with the presence of TAG in the PROFLIN"}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"5.0","i0_calibration_standard":null,"description":"Synchrotron SAXS data from solutions of Profilin (+TAG)  in 20 mM Tris, 50 mM NaCl, pH 8.4 were collected on the B21 beam line at Diamond (Didcot, UK) using an EigerX 4M-Detrics detector at a sample-detector distance of 3.7 m and the wavelength of 0.95 A. The experiment was performed in batch at four dilution, starting at 6.9 mg/ml concentration. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The data didn't presented concentration dependence. Four dilution data were automatically merged by PRIMUS.\r\nThe molecular weight of a Profilin (+TAG), is 18.4 kDa.  In the  Ca-model (GASBOR) was possible not only to fit the PDB model (from 7sbd) but to see the TAG (40 dummy CA) as a long tail, which was next reconstructed by using of CORAL program.","experiment_description":null,"tags":[],"intensity_unit":"1/cm","experimental_mw":20.0,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":20.0,"porod_mw_error":null,"pddf_i0":0.1267,"pddf_i0_error":null,"guinier_i0":0.125199,"guinier_i0_error":null,"pddf_rg":2.09,"pddf_rg_error":null,"guinier_rg":2.0,"guinier_rg_error":0.062,"pddf_dmax":7.43,"pddf_dmax_error":null,"porod_volume":30.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":135,"guinier_point_last":462,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDVH9_datloglog_img.png","symmetry":null,"last_modified":"2025-09-17T10:12:46.881204+02:00","bragg_peak":[]}