{ "code": "SASDAW8", "status": "Published", "type_of_curve": "Extrapolated to infinite dilution", "angular_unit": "1/nm", "project": { "title": "Immunosuppressive Yersinia Effector YopM Binds DEAD Box Helicase DDX3 to Control Ribosomal S6 Kinase in the Nucleus of Host Cells.", "publication": { "title": "Immunosuppressive Yersinia Effector YopM Binds DEAD Box Helicase DDX3 to Control Ribosomal S6 Kinase in the Nucleus of Host Cells.", "author_list": "Berneking L, Schnapp M, Rumm A, Trasak C, Ruckdeschel K, Alawi M, Grundhoff A, Kikhney AG, Koch-Nolte F, Buck F, Perbandt M, Betzel C, Svergun DI, Hentschke M, Aepfelbacher M", "journal": "PLoS Pathog", "doi": "10.1371/journal.ppat.1005660", "pmid": "27300509", "published_date": "2016 Jun" }, "status": "released", "submitted_date": "2015-07-06", "released_date": "2016-06-14" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDAW8.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDAW8.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAW8_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAW8_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDAW8_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAW8_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDAW8.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": "Yersinia outer protein M (34-481)", "short_name": "YopM", "sequence": "KSKTEYYNAWSEWERNAPPGNGEQREMAVSRLRDCLDRQAHELELNNLGLSSLPELPPHLERLVASCNSLTELPELPQSL\r\nKSLEVYENNLKALPDLPPLLVDLRVFNNQLEELPELQNLPFLTEIYANNNSLKTLPDLPPSLVDLNVRENYLTALPELPQ\r\nSLIFLDISDNILSGLSELPPNLSCLDASRNGIRSLCDLPPSLVYLDVRDNQLIELPALPSGLERLIASFNHLAELPELPP\r\nNLYYLDASRNEISSLCDLPPSLVDLNVRKNQLIELPALPPDLERLIASFNHLAELPELPPNLSYLDASRNEISSLCDLPP\r\nSLVDLNVRKNQLIELPALPPDLERLIASFNHLAELPELPPNLSYLDASRNEISSLCDLPPSLVELDVRDNQLIELPALPP\r\nHLERLIASLNHLAEVPELPQNLKQLHVEHNALREFPDIPESVEDLRMD", "organism": "Yersinia enterocolitica", "uniprot_code": null, "uniprot_range_first": 34, "uniprot_range_last": 481, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": null, "mw": 50.321, "total_mw": 100.643, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "DEAD box RNA helicase DDX3 (51-418)", "short_name": "DDX3", "sequence": null, "organism": "Yersinia enterocolitica", "uniprot_code": null, "uniprot_range_first": 51, "uniprot_range_last": 418, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": null, "mw": 41.5, "total_mw": 41.5, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50 mM HEPES 150 mM NaCl", "concentration_unit": "mM", "comment": null, "additive": "150 mM NaCl", "concentration": 50.0, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "2:1 YopM:DDX3 complex", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": false }, "contributor": [ { "affiliation": [ { "short_name": "EMBL-Hamburg", "address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany", "full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation", "webpage": "http://www.embl-hamburg.de/index.php" } ], "contributor_name": "Al", "contributor_surname": "Kikhney", "orcid": "https://orcid.org/0000-0003-1321-3956" } ], "concentration_method": null, "concentration_unit": "mg/ml", "date": "2013-06-14", "storage_temperature": 23.0, "cell_temperature": 23.0, "exposure_time": 0.05, "number_of_frames": 20, "wavelength": 0.12, "sample_detector_distance": 3.1, "concentration_min": 0.66, "concentration_max": 10.6, "sample_volume": null, "flow_rate": null, "s_min": 0.077, "s_max": 4.583, "total_exposure_time": 1.0, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDAW8_fit1_model1_img.png", "software": "SASREF", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDAW8_fit1_model1.pdb", "model_mw": 142.0, "bead_radius": 1.9, "log": null, "symmetry": "", "comment": "", "user": 4 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAW8_fit1_fit_img.png", "software": null, "chi_square_value": 1.547, "p_value": 0.0, "fit_residual_plot": "SASDAW8_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDAW8_fit1.fit", "fit_log": null, "software_version": null, "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDAW8_fit2_model1_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "r5577", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDAW8_fit2_model1.pdb", "model_mw": 123.0, "bead_radius": 3.1, "log": "https://www.sasbdb.org/media/log_files/Hepes_zc_5.log", "symmetry": "", "comment": "", "user": 4 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAW8_fit2_fit_img.png", "software": null, "chi_square_value": 1.344, "p_value": 0.145237, "fit_residual_plot": "SASDAW8_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDAW8_fit2.fir", "fit_log": null, "software_version": null, "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": null, "i0_calibration_standard": null, "description": "A complex composed of two YopM_34-481 molecules and one DDX3_51-418", "experiment_description": null, "tags": [], "intensity_unit": null, "experimental_mw": 123.0, "experimental_mw_error": 12.0, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 119.0, "porod_mw_error": 12.0, "pddf_i0": null, "pddf_i0_error": null, "guinier_i0": 7459.0, "guinier_i0_error": null, "pddf_rg": 4.033, "pddf_rg_error": null, "guinier_rg": 3.97, "guinier_rg_error": 0.12, "pddf_dmax": 15.0, "pddf_dmax_error": 1.5, "porod_volume": 189.7, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 15, "guinier_point_last": 95, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDAW8_datloglog_img.png", "symmetry": null, "last_modified": "2023-06-21T07:56:39.492710+02:00", "bragg_peak": [] }