{"code":"SASDWM2","status":"Published","type_of_curve":"SEC-SAS","angular_unit":"1/A","project":{"title":"Structural basis for the recognition and ubiquitylation of type-2 N-degron substrate by PRT1 plant N-recognin","publication":{"title":"Structural basis for the recognition and ubiquitylation of type-2 N-degron substrate by PRT1 plant N-recognin","author_list":"Yang W, Kim S, Kim M, Shin H, Lee J, Sandmann A, Park O, Dissmeyer N, Song H","journal":"Nature Communications","doi":"10.1038/s41467-025-63282-9","pmid":null,"published_date":"2025 Aug 21"},"status":"released","submitted_date":"2024-11-26","released_date":"2025-08-22"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDWM2.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDWM2.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWM2_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWM2_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDWM2_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWM2_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDWM2.sascif","experiment":{"instrument":{"detector":{"type":null,"name":"Pilatus3 2M","resolution":0.172},"name":"Photon Factory (PF), High Energy Accelerator Research Organization (KEK)","city":"Tsukuba","country":"Japan","beamline_name":"BL-10C","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":"E3 ubiquitin-protein ligase PRT1","short_name":"PRT1","sequence":"MAETMKDITMKNDESQEEEIPDQFLCCVCLELLYKPIVLSCGHLSCFWCVHKSMNGFRESHCPICRDPYVHFPSVCQKLYFLLKKMYPLAHKKREEQVLKEEQERECFSPQIDLVLDLSVCSGDSLNVSDKQKVEECSNAANLLSSSSSRGDIPCIPKNQEPTDAKALNVHENELLKDNKVSKQISKDDLLCSACKELLVRPVVLNCGHVYCEGCVVDMAEESEKIKCQECNVCDPRGFPKVCLILEQLLEENFPEEYNSRSSKVQKTLAHNSKGNIQSYLKEGPSLSNDNNNDDPWLANPGSNVHFGAGCDSCGVYPIIGDRYRCKDCKEEIGYDLCKDCYETPSKVPGRFNQQHTPDHRLELARSPQVLINFNSIGILLGPVISNEGMDTDEGEEGPPGSSNESSSTE","organism":"Arabidopsis thaliana","uniprot_code":"Q8LBL5","uniprot_range_first":1,"uniprot_range_last":410,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MAETMKDITMKNDESQEEEIPDQFLCCVCLELLYKPIVLSCGHLSCFWCVHKSMNGFRES\nHCPICRDPYVHFPSVCQKLYFLLKKMYPLAHKKREEQVLKEEQERECFSPQIDLVLDLSV\nCSGDSLNVSDKQKVEECSNAANLLSSSSSRGDIPCIPKNQEPTDAKALNVHENELLKDNK\nVSKQISKDDLLCSACKELLVRPVVLNCGHVYCEGCVVDMAEESEKIKCQECNVCDPRGFP\nKVCLILEQLLEENFPEEYNSRSSKVQKTLAHNSKGNIQSYLKEGPSLSNDNNNDDPWLAN\nPGSNVHFGAGCDSCGVYPIIGDRYRCKDCKEEIGYDLCKDCYETPSKVPGRFNQQHTPDH\nRLELARSPQVLINFNSIGILLGPVISNEGMDTDEGEEGPPGSSNESSSTE","mw":45.936,"total_mw":45.936,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":""}],"buffer":{"name":"50 mM Tris-HCl, 150 mM NaCl, 1 mM TCEP, 2% w/v glycerol","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":7.5,"deuteration":null},"purity_method":null,"name":"Wild-type E3 ubiquitin-protein ligase PRT1 (Proteolysis1)","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":null,"address":"South Korea","full_name":"Korea University","webpage":"https://www.korea.edu/"}],"contributor_name":"Woo Seok","contributor_surname":"Yang","orcid":"https://orcid.org/0000-0002-0022-0295"}],"concentration_method":null,"concentration_unit":null,"date":"2018-05-22","storage_temperature":25.0,"cell_temperature":25.0,"exposure_time":20.0,"number_of_frames":328,"wavelength":0.15,"sample_detector_distance":3.0,"concentration_min":null,"concentration_max":10.0,"sample_volume":250.0,"flow_rate":0.05,"s_min":0.033,"s_max":2.809,"total_exposure_time":null,"seccolumn":1},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDWM2_fit1_model1_img.png","software":"DAMMIF","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDWM2_fit1_model1.pdb","model_mw":40.042,"bead_radius":null,"log":"https://www.sasbdb.org/media/log_files/final_2_7Z2QyHq.log","symmetry":null,"comment":null,"user":1153}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWM2_fit1_fixed_fit_img.png","software":"DAMMIF","chi_square_value":1.152,"p_value":0.4594,"fit_residual_plot":"SASDWM2_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDWM2_fit1.fir","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/final_2.log","software_version":null,"description":""},{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDWM2_fit2_model1_img.png","software":"AlphaFold Protein Structure Database","pdb_link":[{"pdb_code":"none","ext_code":"Q8LBL5","ext_type":"alphafold","difference_with_model":"identical"}],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDWM2_fit2_model1.pdb","model_mw":46.3,"bead_radius":null,"log":"https://www.sasbdb.org/media/log_files/AF-Q8LBL5-F1-model_v4_5.log","symmetry":null,"comment":null,"user":1153}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWM2_fit2_fixed_fit_img.png","software":"CRYSOL","chi_square_value":1.734,"p_value":0.0,"fit_residual_plot":"SASDWM2_fit2_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDWM2_fit2.fit","fit_log":null,"software_version":null,"description":""}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"5.0","i0_calibration_standard":null,"description":null,"experiment_description":"Synchrotron SAXS data from solutions of PRT1 in 50 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM TCEP, and 2% (w/v) glycerol were collected on the BL-10C beam line at the Photon Factory (PF), High Energy Accelerator Research Organization (KEK; Tsukuba, Japan) using a Pilatus3 2M detector at a sample-detector distance of 3.0 m and at a wavelength of λ = 0.15 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 250.00 μl sample at 10 mg/ml was injected at different flow rates in the protein peak (20 sec/image with flow at 0.05 ml/min) and the base line (20 sec/image with flow at 0.5 ml/min) using a GE Superdex 200 Increase 10/300 column at 25°C. 332 successive 20-second frames were collected.","tags":[],"intensity_unit":"arbitrary","experimental_mw":46.6,"experimental_mw_error":null,"guinier_i0_mw":44.3,"guinier_i0_mw_error":3.9,"porod_mw":38.0,"porod_mw_error":null,"pddf_i0":0.1663,"pddf_i0_error":0.002,"guinier_i0":0.164412,"guinier_i0_error":null,"pddf_rg":3.632,"pddf_rg_error":0.6,"guinier_rg":3.429,"guinier_rg_error":0.58,"pddf_dmax":12.68,"pddf_dmax_error":null,"porod_volume":60.7,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":27,"guinier_point_last":145,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDWM2_datloglog_img.png","symmetry":null,"last_modified":"2025-08-22T03:11:39.462006+02:00","bragg_peak":[]}