The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
Every source field is expanded here, including empty values, list members and fields already shown above.
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{
"code": "SASDBS4",
"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/SASDBS4.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBS4_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBS4_kratky_img.png",
"pddf_plot": null,
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBS4_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBS4.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": "Glutamate decarboxylase alpha (GadA) from E. coli",
"short_name": "GadA",
"sequence": "MDQKLLTDFRSELLDSRFGAKAISTIAESKRFPLHEMRDDVAFQIINDELYLDGNARQNL\r\nATFCQTWDDENVHKLMDLSINKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVG\r\nTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCGPVQICWHKFARYWDVELREI\r\nPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDM\r\nHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELV\r\nFNVDYLGGQIGTFAINFSRPAGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKL\r\nGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSERLRLRGWQVPAFTLGGEATDIVV\r\nMRIMCRRGFEMDFAELLLEDYKASLKYLSDHPKLQGIAQQNSFKHT",
"organism": "Escherichia coli",
"uniprot_code": "P69908",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MDQKLLTDFRSELLDSRFGAKAISTIAESKRFPLHEMRDDVAFQIINDELYLDGNARQNL\nATFCQTWDDENVHKLMDLSINKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVG\nTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCGPVQICWHKFARYWDVELREI\nPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDM\nHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELV\nFNVDYLGGQIGTFAINFSRPAGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKL\nGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSERLRLRGWQVPAFTLGGEATDIVV\nMRIMCRRGFEMDFAELLLEDYKASLKYLSDHPKLQGIAQQNSFKHT",
"mw": 52.685,
"total_mw": 52.685,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "50 mM Tris",
"concentration_unit": "mM",
"comment": null,
"additive": null,
"concentration": 50.0,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Glutamate decarboxylase alpha (GadA) from E. coli, low salt",
"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": null,
"date": "2015-07-29",
"storage_temperature": 10.0,
"cell_temperature": null,
"exposure_time": 0.05,
"number_of_frames": 20,
"wavelength": 0.12,
"sample_detector_distance": 3.1,
"concentration_min": null,
"concentration_max": 5.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.078,
"s_max": 4.001,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBS4_fit1_model1_img.png",
"software": "SASREF MX",
"pdb_link": [
{
"pdb_code": "1xey",
"ext_code": "1XEY",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "mix",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBS4_fit1_model1.pdb",
"model_mw": 303.6,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/oligomer_NQqC6Tv.log",
"symmetry": "P32",
"comment": "",
"user": 94
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBS4_fit1_model2_img.png",
"software": "SASREF MX",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBS4_fit1_model2.pdb",
"model_mw": 101.2,
"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/SASDBS4_fit1_fit_img.png",
"software": null,
"chi_square_value": 1.77,
"p_value": 0.0,
"fit_residual_plot": "SASDBS4_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBS4_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": "Under the experimental conditions described above, GadA exists as a mixture in solution of hexamers (volume fraction approximately 85%) and disassociated dimers (15%). The models displayed for this entry and associated fit are derived from SASREFMX modelling in P32 symmetry. The final fit to the SAXS data of the mixture was determined using OLIGOMER. The specific volume fraction estimates of the hexamer and the dimer are included in the full entry zip archive.",
"experiment_description": "Synchrotron SAXS data from solutions of Glutamate decarboxylase alpha (GadA) 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). A solute concentration of 5 mg/ml was 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 (5 mg/ml). ",
"tags": [],
"intensity_unit": null,
"experimental_mw": 270.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 265.0,
"porod_mw_error": null,
"pddf_i0": null,
"pddf_i0_error": null,
"guinier_i0": 61228.0,
"guinier_i0_error": 64.0,
"pddf_rg": null,
"pddf_rg_error": null,
"guinier_rg": 4.44,
"guinier_rg_error": 0.01,
"pddf_dmax": null,
"pddf_dmax_error": null,
"porod_volume": 450.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 78,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDBS4_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}
