{ "code": "SASDD73", "status": "Published", "type_of_curve": "Merged", "angular_unit": "1/A", "project": { "title": "Structural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans.", "publication": { "title": "Structural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans.", "author_list": "Kryl M, Sedláček V, Kučera I", "journal": "Int J Mol Sci", "doi": "10.3390/ijms24043732", "pmid": "36835143", "published_date": "2023 Feb 13" }, "status": "released", "submitted_date": "2018-01-23", "released_date": "2023-08-31" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDD73.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDD73.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD73_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD73_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDD73_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD73_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDD73.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 100K", "resolution": 172.0 }, "name": "CEITEC", "city": "Brno", "country": "Czech Republic", "beamline_name": "Rigaku BioSAXS-1000", "beam_geometry": "", "type_of_source": "X-ray in house", "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": "NADPH-dependent FMN reductase", "short_name": "Pden_5119", "sequence": "MPGPRIVAFAGSWSRPSKTRSLVEEAARRAVARFGGSAHVFDIADLGPDFGSLRQPQDGP\r\nHTRHLDAFLAADALIVASPVYKGSYTGLFKHFIDLIEPVALVGKPVLLAATGGGDRHALV\r\nIEHQLRPVFGFFEAHTLATGLYVSASDFGPDGLASEAASTRLDRAVAQFAAHLSRHDAAP\r\nLLAVGLEHHHHHH", "organism": "Paracoccus denitrificans", "uniprot_code": "A1BCD5", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MPGPRIVAFAGSWSRPSKTRSLVEEAARRAVARFGGSAHVFDIADLGPDFGSLRQPQDGP\nHTRHLDAFLAADALIVASPVYKGSYTGLFKHFIDLIEPVALVGKPVLLAATGGGDRHALV\nIEHQLRPVFGFFEAHTLATGLYVSASDFGPDGLASEAASTRLDRAVAQFAAHLSRHDAAP\nLLAVG", "mw": 20.596, "total_mw": 41.192, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "Flavin reductase Pden_5119", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": null, "full_name": "CEITEC - Central European Institute of Technology, Masaryk University", "webpage": "https://www.ceitec.eu/" } ], "contributor_name": "Tomas", "contributor_surname": "Klumpler", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2016-02-22", "storage_temperature": 4.0, "cell_temperature": 4.0, "exposure_time": 600.0, "number_of_frames": 30, "wavelength": 0.154, "sample_detector_distance": 0.48, "concentration_min": 1.5, "concentration_max": 7.5, "sample_volume": null, "flow_rate": null, "s_min": 0.152, "s_max": 3.012, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD73_fit1_model2_img.png", "software": "SwissModel", "pdb_link": [ { "pdb_code": "4c76", "ext_code": "4c76", "ext_type": "pdb", "difference_with_model": "derived" } ], "model_title": null, "type_of_model": "atomic", "software_version": "1.1.0", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDD73_fit1_model2.pdb", "model_mw": 36.71, "bead_radius": 1.9, "log": "https://www.sasbdb.org/media/log_files/4c76-homology_model_dimer00.log", "symmetry": "P2", "comment": null, "user": 195 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD73_fit1_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 1.032, "p_value": 0.178897, "fit_residual_plot": "SASDD73_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDD73_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/4c76-homology_model_dimer00.log", "software_version": "2.8.3", "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD73_fit2_model1_img.png", "software": "DAMMIN", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "5.3", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDD73_fit2_model1.pdb", "model_mw": 29.506, "bead_radius": 1.5, "log": "https://www.sasbdb.org/media/log_files/dammin-slow-P2.log", "symmetry": "P2", "comment": null, "user": 195 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD73_fit2_fixed_fit_img.png", "software": "DAMMIN", "chi_square_value": 1.366, "p_value": 0.541867, "fit_residual_plot": "SASDD73_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDD73_fit2.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/dammin-slow-P2.log", "software_version": "5.3", "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": null, "experiment_description": "SAXS data from solutions of flavin reductase Pden_5119 in 50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole, pH 8, were collected on a Rigaku BioSAXS-1000 instrument at the Central European Institute of Technology, CEITEC, (Brno, Czech Republic) using a Pilatus 100K detector at a sample-detector distance of 0.5 m and at a wavelength of λ = 0.154 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1.5 and 7.5 mg/ml were measured at 4°C. 30 successive 600 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 41.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 43.6, "porod_mw_error": null, "pddf_i0": 0.1389, "pddf_i0_error": null, "guinier_i0": 0.14, "guinier_i0_error": 0.0015, "pddf_rg": 2.3, "pddf_rg_error": null, "guinier_rg": 2.34, "guinier_rg_error": 0.098, "pddf_dmax": 6.27, "pddf_dmax_error": null, "porod_volume": 69.8, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 29, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDD73_datloglog_img.png", "symmetry": null, "last_modified": "2023-08-31T11:57:49.604042+02:00", "bragg_peak": [] }