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{
"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": []
}
