{"code":"SASDEE6","status":"Published","type_of_curve":"SEC-SAS","angular_unit":"1/A","project":{"title":"Conformational Flexibility of Ubiquitin-Modified and SUMO-Modified PCNA Shown by Full-Ensemble Hybrid Methods.","publication":{"title":"Conformational Flexibility of Ubiquitin-Modified and SUMO-Modified PCNA Shown by Full-Ensemble Hybrid Methods.","author_list":"Powers KT, Lavering ED, Washington MT","journal":"J Mol Biol","doi":"10.1016/j.jmb.2018.10.017","pmid":"30381149","published_date":"2018 Dec 7"},"status":"released","submitted_date":"2018-10-16","released_date":"2019-05-09"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDEE6.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDEE6.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEE6_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEE6_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEE6_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEE6_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDEE6.sascif","experiment":{"instrument":{"detector":{"type":null,"name":"Pilatus3 X 1M","resolution":0.172},"name":"Advanced Photon Source (APS), Argonne National Laboratory","city":"Lemont, IL","country":"USA","beamline_name":"BioCAT 18ID","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":"Proliferating cell nuclear antigen","short_name":"PCNA","sequence":"MGSSHHHHHHSQDPMSDSEVNQEAKPEVKPEVKPET\r\nHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLD\r\nMEDNDIIEAHREQIGGPGETIKFVADGDIGSGSVIIKPFVDMEHPETSIKLEMDQPVDLT\r\nFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKSGFLQFFLAPKFNDEE\r\nMLEAKFE\r\nEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGVEAFQEYRCDHPVT\r\nLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKLMDIDADFLK\r\nIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMIT","organism":"Saccharomyces cerevisiae","uniprot_code":"P15873","uniprot_range_first":null,"uniprot_range_last":null,"oligomerization":"trimer","molecular_type":"protein","uniprot_sequence":"MLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGVEAFQEY\nRCDHPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKLMD\nIDADFLKIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMITKETIKFVADGDIGSGSV\nIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFD\nLKSGFLQFFLAPKFNDEE","mw":41.798,"total_mw":125.394,"number_molecules":3,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"20 mM Tris, 150 mM NaCl, 5% glycerol, 1 mM TCEP","concentration_unit":null,"comment":"22C","additive":null,"concentration":null,"pka":null,"ph":7.5,"deuteration":null},"purity_method":null,"name":"Proliferating cell nuclear antigen - SUMOPCNA - Split Fusion Trimer","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":null,"address":"Iowa, USA","full_name":"University of Iowa Carver College of Medicine","webpage":"https://medicine.uiowa.edu/"}],"contributor_name":"Kyle","contributor_surname":"Powers","orcid":""}],"concentration_method":null,"concentration_unit":null,"date":"2018-08-06","storage_temperature":22.0,"cell_temperature":22.0,"exposure_time":0.5,"number_of_frames":320,"wavelength":0.1033,"sample_detector_distance":3.5,"concentration_min":0.0,"concentration_max":32.5,"sample_volume":null,"flow_rate":null,"s_min":0.055,"s_max":3.857,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDEE6_fit1_model1_img.png","software":"UIOWA_BD","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDEE6_fit1_model1.pdb","model_mw":null,"bead_radius":null,"log":null,"symmetry":null,"comment":"One representative PDB from the simulation.","user":377}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/EnsembleSUMO_fit_img.png","software":"CRYSOL","chi_square_value":2.581,"p_value":0.0,"fit_residual_plot":"EnsembleSUMO_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDEE6_fit1.fit","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/nohup_eMzMQqx.out","software_version":"2.7.2","description":"This is a fit derived from 10,000 crysol fit calculations using full simulation ensemble. The log file is reflective of this including all of the individual crysol calculations."}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"5.0","i0_calibration_standard":null,"description":null,"experiment_description":"Synchrotron SAXS data were collected using size-exclusion chromatography SAXS (SEC-SAXS) on the BioCAT 18-ID beam line at the Advanced Photon Source (APS), Argonne National Laboratory (Lemont, IL, USA). Data were acquired using a reverse-biased silicon diode array Pilatus3 1M detector at a sample-detector distance of 3.5 m and at a wavelength of λ = 0.1033 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Poly-histidine tagged SUMO-proliferating cell nuclear antigen (SUMOPCNA) was measured as a split fusion protein (PCNA (1-163, His-SUMO-165-258) at a sample injection concentration of 32.5 mg/ml at 22°C using a Wyatt Technology WTC-030S5 (SN 0787), WTC - 015 S5 column with a sample injection volume of 500μL sample at a flow-rate of 0.9 mL/min. The mobile phase was 20 mM Tris, 150 mM NaCl, 5% glycerol, 1 mM TCEP, pH 7.5. 320 successive 0.500 second SAXS data frames were collected through the SEC-elution profile that underwent appropriate date reduction, background correction (buffer subtraction) scaling and averaging to generate the profile displayed in this entry. The model represents a one state from an ensemble trajectory of SUMO-modified PCNA. The full ensemble is included in the full-entry zip archive (ca. 300 MB).","tags":[],"intensity_unit":"arbitrary","experimental_mw":125.4,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":194.0,"porod_mw_error":null,"pddf_i0":326.4,"pddf_i0_error":null,"guinier_i0":324.9,"guinier_i0_error":0.5,"pddf_rg":4.65,"pddf_rg_error":null,"guinier_rg":4.653,"guinier_rg_error":0.08,"pddf_dmax":16.92,"pddf_dmax_error":null,"porod_volume":310.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":7,"guinier_point_last":74,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDEE6_datloglog_img.png","symmetry":null,"last_modified":"2019-12-06T13:07:15.624532+01:00","bragg_peak":[]}