{"code":"SASDVC6","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/SASDVC6.dat","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDVC6.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVC6_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVC6_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVC6_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVC6_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDVC6.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 (C317S, C318S)","short_name":"Half-PTX3","sequence":"ENSDDYDLMYVNLDNEIDNGLHPTEDPTPCACGQEHSEWDKLFIMLENSQMRERMLLQATDDVLRGELQR LREELGRLAESLARPCAPGAPAEARLTSALDELLQATRDAGRRLARMEGAEAQRPEEAGRALAAVLEELRQTRADLHAVQGWAARSWLPAGCETAILFPMRSKKIFGSVHPVRPMRLESFSACIWVKATDVLNKTILFSYGTKRNPYEIQLYLSYQSIVFVVGGEENKLVAEAMVSLGRWTHLCGTWNSEEGLTSLWVNGELAATTVEMATGHIVPEGGILQIGQEKNGSSVGGGFDETLAFSGRLTGFNIWDSVLSNEEIRETGGAESCHIRGNIVGWGVTEIQPHGGAQYVS","organism":"Homo sapiens","uniprot_code":"P26022","uniprot_range_first":18,"uniprot_range_last":381,"oligomerization":"tetramer","molecular_type":"protein","uniprot_sequence":"MHLLAILFCALWSAVLAENSDDYDLMYVNLDNEIDNGLHPTEDPTPCACGQEHSEWDKLF\nIMLENSQMRERMLLQATDDVLRGELQRLREELGRLAESLARPCAPGAPAEARLTSALDEL\nLQATRDAGRRLARMEGAEAQRPEEAGRALAAVLEELRQTRADLHAVQGWAARSWLPAGCE\nTAILFPMRSKKIFGSVHPVRPMRLESFSACIWVKATDVLNKTILFSYGTKRNPYEIQLYL\nSYQSIVFVVGGEENKLVAEAMVSLGRWTHLCGTWNSEEGLTSLWVNGELAATTVEMATGH\nIVPEGGILQIGQEKNGCCVGGGFDETLAFSGRLTGFNIWDSVLSNEEIRETGGAESCHIR\nGNIVGWGVTEIQPHGGAQYVS","mw":40.089,"total_mw":160.356,"number_molecules":4,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":"Half-PTX3 was expressed in human embryonic kidney (HEK) Expi293F cells and is therefore glycosylated.\r\nSignal sequence cleaved (amino acids 1-17 of UniProt P26022). A48 isoform. Amino acids C317 and C318 mutated to serine."}],"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":"Tetramer of Pentraxin-3","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":0.026,"s_max":3.4,"total_exposure_time":null,"seccolumn":59},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDVC6_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/SASDVC6_fit1_model1.pdb","model_mw":172.3,"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/SASDVC6_fit1_fixed_fit_img.png","software":"FoXS","chi_square_value":37.543753,"p_value":0.0,"fit_residual_plot":"SASDVC6_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDVC6_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 (tetramers) 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 0.08 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":181.359,"experimental_mw_error":null,"guinier_i0_mw":221.504,"guinier_i0_mw_error":null,"porod_mw":null,"porod_mw_error":null,"pddf_i0":14507.64,"pddf_i0_error":null,"guinier_i0":0.242423,"guinier_i0_error":null,"pddf_rg":7.94,"pddf_rg_error":null,"guinier_rg":7.79,"guinier_rg_error":1.351,"pddf_dmax":26.0,"pddf_dmax_error":null,"porod_volume":370.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":39,"guinier_point_last":61,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDVC6_datloglog_img.png","symmetry":null,"last_modified":"2025-07-27T15:24:02.710000+02:00","bragg_peak":[]}