{"code":"SASDFC2","status":"Published","type_of_curve":"Extrapolated to infinite dilution","angular_unit":"1/nm","project":{"title":"Did evolution create a flexible ligand-binding cavity in the urokinase receptor through deletion of a plesiotypic disulfide bond?","publication":{"title":"Did evolution create a flexible ligand-binding cavity in the urokinase receptor through deletion of a plesiotypic disulfide bond?","author_list":"Leth JM, Mertens HDT, Leth-Espensen KZ, Jørgensen TJD, Ploug M","journal":"J Biol Chem","doi":"10.1074/jbc.RA119.007847","pmid":"30894413","published_date":"2019 Mar 20"},"status":"released","submitted_date":"2019-01-30","released_date":"2019-03-20"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDFC2.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDFC2.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFC2_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFC2_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFC2_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFC2_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDFC2.sascif","experiment":{"instrument":{"detector":{"type":null,"name":"Pilatus 2M","resolution":null},"name":"PETRA III","city":"DESY; Hamburg","country":"Germany","beamline_name":"EMBL P12","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":"Urokinase plasminogen activator surface receptor","short_name":"uPAR","sequence":">sp|Q03405|UPAR_HUMAN Urokinase plasminogen activator surface receptor OS=Homo sapiens GN=PLAUR PE=1 SV=1\nMGHPPLLPLLLLLHTCVPASWGLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEEL\nELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISC\nGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNG\nFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGP\nMNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDV\nQYRSGAAPQPGPAHLSLTITLLMTARLWGGTLLWT\n\n","organism":"Homo sapiens","uniprot_code":"Q03405","uniprot_range_first":null,"uniprot_range_last":null,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MGHPPLLPLLLLLHTCVPASWGLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEEL\nELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISC\nGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNG\nFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGP\nMNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDV\nQYRSGAAPQPGPAHLSLTITLLMTARLWGGTLLWT","mw":36.98,"total_mw":36.98,"number_molecules":1,"complex_state":null,"deuteration":null,"molecule_source":"biological","molecule_description":null},{"long_name":"Urokinase-type plasminogen activator (Amino Terminal Fragment)","short_name":"ATF","sequence":"MRALLARLLL CVLVVSDSKG SNELHQVPSN CDCLNGGTCV SNKYFSNIHW \r\nCNCPKKFGGQ HCEIDKSKTC YEGNGHFYRG KASTDTMGRP CLPWNSATVL \r\nQQTYHAHRSD ALQLGLGKHN YCRNPDNRRR PWCYVQVGLK PLV","organism":"Homo sapiens","uniprot_code":"P00749","uniprot_range_first":1,"uniprot_range_last":143,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MRALLARLLLCVLVVSDSKGSNELHQVPSNCDCLNGGTCVSNKYFSNIHWCNCPKKFGGQ\nHCEIDKSKTCYEGNGHFYRGKASTDTMGRPCLPWNSATVLQQTYHAHRSDALQLGLGKHN\nYCRNPDNRRRPWCYVQVGLKPLVQECMVHDCADGKKPSSPPEELKFQCGQKTLRPRFKII\nGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLG\nRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTICL\nPSMYNDPQFGTSCEITGFGKENSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKML\nCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIR\nSHTKEENGLAL","mw":16.099,"total_mw":16.099,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"20 mM PBS, 5 %(v/v) glycerol","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":7.4,"deuteration":null},"purity_method":null,"name":"Urokinase plasminogen activator surface receptor, uPAR K50C-V70C, complex with urokinase-type plasminogen activator (Amino Terminal Fragment, ATF).","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":"EMBL-Hamburg","address":"Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany","full_name":"European Molecular Biology Laboratory (EMBL) - Hamburg outstation","webpage":"http://www.embl-hamburg.de/index.php"}],"contributor_name":"Haydyn","contributor_surname":"Mertens","orcid":null}],"concentration_method":null,"concentration_unit":null,"date":"2017-05-05","storage_temperature":10.0,"cell_temperature":10.0,"exposure_time":0.05,"number_of_frames":20,"wavelength":0.124,"sample_detector_distance":3.1,"concentration_min":0.3,"concentration_max":2.5,"sample_volume":null,"flow_rate":null,"s_min":0.023,"s_max":5.035,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDFC2_fit1_model1_img.png","software":"DAMMIN","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDFC2_fit1_model1.pdb","model_mw":45.086,"bead_radius":3.0,"log":"https://www.sasbdb.org/media/log_files/ref2.log","symmetry":null,"comment":"Refined DAMMIN model from average volume (10 DAMMIF iterations)","user":12}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/ref2_fit_img.png","software":"DAMMIN","chi_square_value":1.433,"p_value":0.121868,"fit_residual_plot":"ref2_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDFC2_fit1.fir","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/ref2.log","software_version":"5.3","description":"Refined DAMMIN model from average volume (10 DAMMIF iterations)"}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"5.0","i0_calibration_standard":null,"description":"Introduced disulfide in the first LU domain, DI, of uPAR (K50C-V70C).","experiment_description":"Synchrotron SAXS data from solutions of uPAR K50C-V70C in complex with uPA-ATF in 20 mM PBS, 5 %(v/v) glycerol, pH 7.4 were collected on the EMBL P12 beam line at PETRA III (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3.1 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.3 and 2.5 mg/ml were measured at 10°C. 20 successive 0.050 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The low angle data collected at lower concentrations were extrapolated to infinite dilution and merged with the higher concentration data to yield the final composite scattering curve.","tags":[],"intensity_unit":"1/cm","experimental_mw":51.9,"experimental_mw_error":null,"guinier_i0_mw":51.9,"guinier_i0_mw_error":null,"porod_mw":38.6,"porod_mw_error":null,"pddf_i0":0.04019,"pddf_i0_error":0.001,"guinier_i0":0.04024,"guinier_i0_error":0.001,"pddf_rg":2.659,"pddf_rg_error":0.01,"guinier_rg":2.64,"guinier_rg_error":0.01,"pddf_dmax":9.0,"pddf_dmax_error":0.5,"porod_volume":65.6,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":1,"guinier_point_last":146,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDFC2_datloglog_img.png","symmetry":null,"last_modified":"2023-06-21T07:56:39.492710+02:00","bragg_peak":[]}