{"code":"SASDVB6","status":"Published","type_of_curve":"SEC-SAS","angular_unit":"1/A","project":{"title":"The structural organisation of pentraxin-3 and its interactions with heavy chains of inter-α-inhibitor regulate crosslinking of the hyaluronan matrix","publication":{"title":"The structural organisation of pentraxin-3 and its interactions with heavy chains of inter-α-inhibitor regulate crosslinking of the hyaluronan matrix","author_list":"Shah A, Zhang X, Snee M, Lockhart-Cairns M, Levy C, Jowitt T, Birchenough H, Dean L, Collins R, Dodd R, Roberts A, Enghild J, Mantovani A, Fontana J, Baldock C, Inforzato A, Richter R, Day A","journal":"Matrix Biology","doi":"10.1016/j.matbio.2025.01.002","pmid":null,"published_date":"2025 Apr"},"status":"released","submitted_date":"2024-08-19","released_date":"2025-07-27"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDVB6.dat","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDVB6.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVB6_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVB6_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVB6_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVB6_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDVB6.sascif","experiment":{"instrument":{"detector":{"type":null,"name":"Pilatus 2M","resolution":null},"name":"Diamond Light Source","city":"Didcot","country":"UK","beamline_name":"B21","beam_geometry":"1 x 5 mm","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":"Pentraxin-related protein PTX3 (N-terminal deletion mutant)","short_name":"Δ1-24 PTX3","sequence":"ELEDPTPCACGQEHSEWDKLFIMLENSQMRERMLLQATDDVLRGELQRLREELGRLAESL         \r\nARPCAPGAPAEARLTSALDELLQATRDAGRRLARMEGAEAQRPEEAGRALAAVLEELRQT       \r\nRADLHAVQGWAARSWLPAGCETAILFPMRSKKIFGSVHPVRPMRLESFSACIWVKATDVL        \r\nNKTILFSYGTKRNPYEIQLYLSYQSIVFVVGGEENKLVAEAMVSLGRWTHLCGTWNSEEG        \r\nLTSLWVNGELAATTVEMATGHIVPEGGILQIGQEKNGCCVGGGFDETLAFSGRLTGFNIW \r\nDSVLSNEEIRETGGAESCHIRGNIVGWGVTEIQPHGGAQYVS","organism":"Homo sapiens","uniprot_code":"P26022","uniprot_range_first":42,"uniprot_range_last":381,"oligomerization":"octamer","molecular_type":"protein","uniprot_sequence":"MHLLAILFCALWSAVLAENSDDYDLMYVNLDNEIDNGLHPTEDPTPCACGQEHSEWDKLF\nIMLENSQMRERMLLQATDDVLRGELQRLREELGRLAESLARPCAPGAPAEARLTSALDEL\nLQATRDAGRRLARMEGAEAQRPEEAGRALAAVLEELRQTRADLHAVQGWAARSWLPAGCE\nTAILFPMRSKKIFGSVHPVRPMRLESFSACIWVKATDVLNKTILFSYGTKRNPYEIQLYL\nSYQSIVFVVGGEENKLVAEAMVSLGRWTHLCGTWNSEEGLTSLWVNGELAATTVEMATGH\nIVPEGGILQIGQEKNGCCVGGGFDETLAFSGRLTGFNIWDSVLSNEEIRETGGAESCHIR\nGNIVGWGVTEIQPHGGAQYVS","mw":37.584,"total_mw":300.672,"number_molecules":8,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":"Δ1-24 PTX3 was expressed in human embryonic kidney (HEK) Expi293F cells and is therefore glycosylated. The amino acid numbering of the deletion mutant (Δ1-24) refers to the amino acid numbering of the mature protein, i.e., after the signal sequence has been cleaved (and therefore this construct corresponds to the removal of amino acids 1-17 (signal sequence) and 18-41 (Δ1-24) from the UniProt P26022 reference sequence). A48 isoform. The protein construct used for SAXS also contains and additional two non-native amino acids at the N-terminus (EL)."}],"buffer":{"name":"137 mM NaCl, 2.7 mM KCl, 10 mM phosphate buffer","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":7.4,"deuteration":null},"purity_method":null,"name":"Pentraxin-3 truncation mutant lacking the first 24 amino acids per mature promoter","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":null,"address":"Manchester, UK","full_name":"University of Manchester","webpage":"http://www.manchester.ac.uk/"}],"contributor_name":"Anokhi","contributor_surname":"Shah","orcid":"https://orcid.org/0000-0001-9818-5573"}],"concentration_method":null,"concentration_unit":null,"date":"2020-02-06","storage_temperature":4.0,"cell_temperature":20.0,"exposure_time":1.0,"number_of_frames":620,"wavelength":0.095,"sample_detector_distance":2.7,"concentration_min":null,"concentration_max":8.5,"sample_volume":45.0,"flow_rate":0.08,"s_min":0.06,"s_max":2.142,"total_exposure_time":null,"seccolumn":59},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDVB6_fit1_model1_img.png","software":"AllosMod","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDVB6_fit1_model1.pdb","model_mw":323.0,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":1107}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVB6_fit1_fixed_fit_img.png","software":"FoXS","chi_square_value":25.471879,"p_value":0.0,"fit_residual_plot":"SASDVB6_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDVB6_fit1.fit","fit_log":null,"software_version":null,"description":""}],"estimated_volume_method":null,"pddf_software":"ScÅtter","pddf_software_version":null,"i0_calibration_standard":null,"description":null,"experiment_description":"Synchrotron SAXS data from solutions of Pentraxin-3 (N-terminal deletion mutant) in 137 mM NaCl, 2.7 mM KCl, 10 mM phosphate buffer, pH 7.4 were collected on the B21 beam line at the Diamond Light Source (Didcot, UK) using a Pilatus 2M detector at a sample-detector distance of 2.7 m and at a wavelength of λ = 0.095 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 8.5 mg/ml was injected at a 0.075 ml/min flow rate onto a Cytiva Superose 6 Increase 3.2/300 column at 20°C. 620 successive 1 second frames were collected throughout the entire SEC elution. 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":"arbitrary","experimental_mw":331.621,"experimental_mw_error":null,"guinier_i0_mw":384.929,"guinier_i0_mw_error":null,"porod_mw":null,"porod_mw_error":null,"pddf_i0":26574.02,"pddf_i0_error":null,"guinier_i0":0.260703,"guinier_i0_error":null,"pddf_rg":9.52,"pddf_rg_error":null,"guinier_rg":8.372,"guinier_rg_error":0.64,"pddf_dmax":40.0,"pddf_dmax_error":null,"porod_volume":647.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":15,"guinier_point_last":55,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDVB6_datloglog_img.png","symmetry":null,"last_modified":"2025-07-27T15:24:02.558358+02:00","bragg_peak":[]}