{ "code": "SASDGB6", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/A", "project": { "title": "Large-scale conformational rearrangement of the α5-helix of Gα subunits in complex with the guanine nucleotide exchange factor Ric8A.", "publication": { "title": "Large-scale conformational rearrangement of the α5-helix of Gα subunits in complex with the guanine nucleotide exchange factor Ric8A.", "author_list": "Srivastava D, Artemyev NO", "journal": "J Biol Chem", "doi": "10.1074/jbc.AC119.011135", "pmid": "31624147", "published_date": "2019 Oct 17" }, "status": "released", "submitted_date": "2019-09-26", "released_date": "2019-11-04" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDGB6.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDGB6.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGB6_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGB6_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDGB6_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGB6_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDGB6.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus3 X 1M", "resolution": 0.172 }, "name": "Advanced Photon Source (APS), Argonne National Laboratory", "city": "Lemont, IL", "country": "USA", "beamline_name": "BioCAT 18ID", "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": "Resistance to inhibitors of cholinesterase 8 homolog A", "short_name": "Ric8a", "sequence": "GHMADPRAVADALETGEEDVVMEALRAYNRENSQSFTFDDAQQEDRKRLAKLLVSVLEQGLPP\r\nSRRVIWLQSIRILSRDRSCLDSFTSRRSLQALACYAGISASQGSVPEPLNMDVVLESLKC\r\nLCNLVLSSPVAQALAAEAGLVVRLAERVGLCRQSSFPHDVQFFDLRLLFLLTALRTDVRQ\r\nQLFQELQGVRLLTRALELTLGMTEGERHPELLPPQETERAMEILKVLFNITFDSIKREVD\r\nEEDAALYRHLGTLLRHCVMLAAAGDRTEELHGHAVNLLGNLPVKCLDVLLTLEPHEGSLE\r\nFLGVNMDVIRVLLSFMEKRLHQTHRLKESVAPVLSVLTECARMHRPARKFLKAQVLPPLR\r\nDVRTRPEVGELLRNKLVRLMTHLDTDVKRVAAEFLFVLCSESVPRFIKYTGYGNAAGLLA\r\nARGLMAGGRPEGQYSEDEDTDTDEYKEAKASINPVTGRVEEKPPNPMEGMTEEQKEHEAM\r\nKLVNMFDKLSRH", "organism": "Bos taurus", "uniprot_code": "Q5E9J8", "uniprot_range_first": 1, "uniprot_range_last": 492, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MEPRAVADALETGEEDVVMEALRAYNRENSQSFTFDDAQQEDRKRLAKLLVSVLEQGLPP\nSRRVIWLQSIRILSRDRSCLDSFTSRRSLQALACYAGISASQGSVPEPLNMDVVLESLKC\nLCNLVLSSPVAQALAAEAGLVVRLAERVGLCRQSSFPHDVQFFDLRLLFLLTALRTDVRQ\nQLFQELQGVRLLTRALELTLGMTEGERHPELLPPQETERAMEILKVLFNITFDSIKREVD\nEEDAALYRHLGTLLRHCVMLAAAGDRTEELHGHAVNLLGNLPVKCLDVLLTLEPHEGSLE\nFLGVNMDVIRVLLSFMEKRLHQTHRLKESVAPVLSVLTECARMHRPARKFLKAQVLPPLR\nDVRTRPEVGELLRNKLVRLMTHLDTDVKRVAAEFLFVLCSESVPRFIKYTGYGNAAGLLA\nARGLMAGGRPEGQYSEDEDTDTDEYKEAKASINPVTGRVEEKPPNPMEGMTEEQKEHEAM\nKLVNMFDKLSRHRVIQPMGMSPRGQLTSLQDAMCETMEGQLSSDPDSDPD", "mw": 55.643, "total_mw": 55.643, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "miniGi", "short_name": null, "sequence": "AMEKAAREVKLLLLGADNSGKSTIVKQMKIIHEAGEYMPMERVKTTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEDVAAIIFCVDLSDYEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYQEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF", "organism": "synthetic construct", "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": null, "mw": 24.54, "total_mw": 24.54, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM Tris, 150 mM KCl, 5 % glycerol, 1 mM TCEP", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "Resistance to inhibitors of cholinesterase 8 homolog A (Ric8A) miniGi complex", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Iowa, USA", "full_name": "University of Iowa", "webpage": "https://uiowa.edu/" } ], "contributor_name": "Dhiraj", "contributor_surname": "Srivastava", "orcid": "" } ], "concentration_method": null, "concentration_unit": null, "date": "2018-10-27", "storage_temperature": 4.0, "cell_temperature": null, "exposure_time": 0.5, "number_of_frames": null, "wavelength": null, "sample_detector_distance": null, "concentration_min": null, "concentration_max": 10.0, "sample_volume": 250.0, "flow_rate": 0.9, "s_min": 0.039, "s_max": 3.813, "total_exposure_time": null, "seccolumn": 1 }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDGB6_fit1_model1_img.png", "software": "Other", "pdb_link": [ { "pdb_code": "6n85", "ext_code": "6N85", "ext_type": "pdb", "difference_with_model": "derived" } ], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDGB6_fit1_model1.pdb", "model_mw": null, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 431 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/86900_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 1.637, "p_value": 0.0, "fit_residual_plot": "86900_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDGB6_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/86900.log", "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDGB6_fit2_model1_img.png", "software": "Rosetta", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "Rosetta", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDGB6_fit2_model1.pdb", "model_mw": 79.71, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 431 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/73700_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 1.882, "p_value": 0.0, "fit_residual_plot": "73700_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDGB6_fit2.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/73700.log", "software_version": null, "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "4.6", "i0_calibration_standard": null, "description": "Purified Ric8a1-492 was mixed with excess of purified miniGi and the complex was purified by size-exclusion chromatography (SEC). The complex fractions were pooled together, concentrated and additional SEC-SAXS data was collected as described above. X-ray wavelength = UNKNOWN.", "experiment_description": "Synchrotron SAXS data from solutions of the Ric8A-miniGi complex in 20 mM Tris, 150 mM KCl, 5 % glycerol, 1 mM TCEP, pH 8 were collected on the BioCAT 18ID beam line at the Advanced Photon Source (APS), Argonne National Laboratory storage ring (Lemont, IL, USA) using a Pilatus3 X 1M detector (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 250.00 μl sample at 10 mg/ml was injected at a 0.90 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column . The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 83.6, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 0.00261, "pddf_i0_error": 1.93e-06, "guinier_i0": 0.0026, "guinier_i0_error": 2.65e-06, "pddf_rg": 3.28, "pddf_rg_error": 0.003, "guinier_rg": 3.24, "guinier_rg_error": 0.006, "pddf_dmax": 10.7, "pddf_dmax_error": null, "porod_volume": null, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 13, "guinier_point_last": 118, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDGB6_datloglog_img.png", "symmetry": null, "last_modified": "2021-01-04T14:24:46.462986+01:00", "bragg_peak": [] }