{ "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": [] }