{"code":"SASDB23","status":"Published","type_of_curve":"Single concentration","angular_unit":"1/nm","project":{"title":"X-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism.","publication":{"title":"X-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism.","author_list":"Dadinova LA, Shtykova EV, Konarev PV, Rodina EV, Snalina NE, Vorobyeva NN, Kurilova SA, Nazarova TI, Jeffries CM, Svergun DI","journal":"PLoS One","doi":"10.1371/journal.pone.0156105","pmid":"27227414","published_date":"2016"},"status":"released","submitted_date":"2015-12-14","released_date":"2016-07-01"},"pddf_data":null,"intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDB23.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB23_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB23_kratky_img.png","pddf_plot":null,"intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB23_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDB23.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":"5-keto-4-deoxyuronate isomerase (KduI) from E. coli","short_name":"Kdu1","sequence":"MDVRQSIHSAHAKTLDTQGLRNEFLVEKVFVADEYTMVYSHIDRIIVGGIMPITKTVSVG\r\nGEVGKQLGVSYFLERRELGVINIGGAGTITVDGQCYEIGHRDALYVGKGAKEVVFASIDT\r\nGTPAKFYYNCAPAHTTYPTKKVTPDEVSPVTLGDNLTSNRRTINKYFVPDVLETCQLSMG\r\nLTELAPGNLWNTMPCHTHERRMEVYFYFNMDDDACVFHMMGQPQETRHIVMHNEQAVISP\r\nSWSIHSGVGTKAYTFIWGMVGENQVFDDMDHVAVKDLR","organism":"Escherichia coli","uniprot_code":"Q46938","uniprot_range_first":null,"uniprot_range_last":null,"oligomerization":null,"molecular_type":"protein","uniprot_sequence":"MDVRQSIHSAHAKTLDTQGLRNEFLVEKVFVADEYTMVYSHIDRIIVGGIMPITKTVSVG\nGEVGKQLGVSYFLERRELGVINIGGAGTITVDGQCYEIGHRDALYVGKGAKEVVFASIDT\nGTPAKFYYNCAPAHTTYPTKKVTPDEVSPVTLGDNLTSNRRTINKYFVPDVLETCQLSMG\nLTELAPGNLWNTMPCHTHERRMEVYFYFNMDDDACVFHMMGQPQETRHIVMHNEQAVISP\nSWSIHSGVGTKAYTFIWGMVGENQVFDDMDHVAVKDLR","mw":31.076,"total_mw":null,"number_molecules":null,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"50 mM Tris 10 mM NaCl","concentration_unit":"mM","comment":null,"additive":"10 mM NaCl","concentration":50.0,"pka":null,"ph":7.5,"deuteration":null},"purity_method":null,"name":"5-keto-4-deoxyuronate isomerase (KduI) from E. coli","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":"MSU","address":"Moscow, Russia","full_name":"Lomonosov Moscow State University","webpage":"http://www.msu.ru"}],"contributor_name":"Liubov","contributor_surname":"Dadinova","orcid":null}],"concentration_method":null,"concentration_unit":"mg/ml","date":"2013-06-20","storage_temperature":10.0,"cell_temperature":10.0,"exposure_time":0.05,"number_of_frames":20,"wavelength":0.12,"sample_detector_distance":3.1,"concentration_min":1.4,"concentration_max":10.8,"sample_volume":null,"flow_rate":null,"s_min":0.106,"s_max":4.02,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/1kdu_img.png","software":"OLIGOMER","pdb_link":[],"model_title":null,"type_of_model":"mix","software_version":"","model_data":"https://www.sasbdb.org/media/pdb_file/SASDB23_fit1_model1.pdb","model_mw":63.99,"bead_radius":1.9,"log":null,"symmetry":"","comment":"","user":94},{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/Kdu_full_O65k7z7_img.png","software":"OLIGOMER","pdb_link":[{"pdb_code":"1xru","ext_code":"1XRU","ext_type":"pdb","difference_with_model":"identical"}],"model_title":null,"type_of_model":"mix","software_version":"","model_data":"https://www.sasbdb.org/media/pdb_file/SASDB23_fit1_model2.pdb","model_mw":192.0,"bead_radius":1.9,"log":null,"symmetry":"","comment":"","user":94},{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/2kdu_full_2qx2r5q_img.png","software":"OLIGOMER","pdb_link":[],"model_title":null,"type_of_model":"mix","software_version":"","model_data":"https://www.sasbdb.org/media/pdb_file/SASDB23_fit1_model3.pdb","model_mw":384.0,"bead_radius":1.9,"log":null,"symmetry":"","comment":"","user":94},{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/KduI_extended_2_hiGoFFL_img.png","software":"OLIGOMER","pdb_link":[],"model_title":null,"type_of_model":"mix","software_version":"","model_data":"https://www.sasbdb.org/media/pdb_file/SASDB23_fit1_model4.pdb","model_mw":384.0,"bead_radius":1.9,"log":null,"symmetry":"","comment":"","user":94}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDB23_fit1_fit_img.png","software":null,"chi_square_value":1.77,"p_value":0.0,"fit_residual_plot":"SASDB23_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDB23_fit1.fit","fit_log":null,"software_version":null,"description":null}],"estimated_volume_method":null,"pddf_software":null,"pddf_software_version":null,"i0_calibration_standard":null,"description":"KduI exists of a mixture of species in solution that include dimers, hexamers and dodecamers. The modelling results from OLIGOMER are displayed where, in terms of volume fraction, the KduI sample consists of approximately:  30% dimers, 30% hexamers; 15% stacked dodecamers and 25% extended dodecamers. The OLIGOMER results are included in the zip archive for this entry. In addition, the Guinier plot at low-s2 is non linear. Two regions in the plot can be identified: s2, 0.01–0.035 and 0.04–0.11 nm-2, from which two values of Rg can be approximated (6.2 nm and 4.5 nm).","experiment_description":"Synchrotron SAXS data from solutions of 5-keto-4-deoxyuronate isomerase (KduI) from E. coli in 50 mM Tris, pH 7.5 were collected on the P12 beam line of Petra-III (Hamburg, Germany) using a Pilatus 2M detector (I(s) vs s; s = 4π sin θ/λ, where 2θ is the scattering angle and λ=0.124 nm). Different solute concentrations in the range 2.7-11.80 mg/ml were measured using an exposure time of 1 s (recorded as 20 x 0.050 s frames). The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering from the matched solvent-blank was subtracted. The data presented here are from a single concentration scattering curve (4.0 mg/ml).","tags":[],"intensity_unit":null,"experimental_mw":183.0,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":null,"porod_mw_error":null,"pddf_i0":null,"pddf_i0_error":null,"guinier_i0":9573.0,"guinier_i0_error":25.0,"pddf_rg":null,"pddf_rg_error":null,"guinier_rg":4.54,"guinier_rg_error":0.01,"pddf_dmax":null,"pddf_dmax_error":null,"porod_volume":null,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":37,"guinier_point_last":87,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDB23_datloglog_img.png","symmetry":null,"last_modified":"2023-06-21T07:56:39.492710+02:00","bragg_peak":[]}