{ "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": [] }