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{
"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": []
}
