{ "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": [] }