{ "code": "SASDCS6", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/A", "project": { "title": "Conformational States of Exchange Protein Directly Activated by cAMP (EPAC1) Revealed by Ensemble Modeling and Integrative Structural Biology.", "publication": { "title": "Conformational States of Exchange Protein Directly Activated by cAMP (EPAC1) Revealed by Ensemble Modeling and Integrative Structural Biology.", "author_list": "White MA, Tsalkova T, Mei FC, Cheng X", "journal": "Cells", "doi": "10.3390/cells9010035", "pmid": "31877746", "published_date": "2019 Dec 21" }, "status": "released", "submitted_date": "2017-07-27", "released_date": "2019-12-02" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDCS6.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCS6.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCS6_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCS6_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCS6_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCS6_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCS6.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 100K", "resolution": 172.0 }, "name": "Sealy Center For Structural Biology, UTMB-G", "city": "Galveston, TX", "country": "USA", "beamline_name": "Rigaku BioSAXS-1000", "beam_geometry": null, "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": "Rap guanine nucleotide exchange factor 3", "short_name": "EPAC1B", "sequence": "GSPGIRVL\r\nVLRRMHRPRSCSYQLLLEHQRPSCIQGLRWTPLTNSEESLDFSES\r\nLEQASTERVLRAGRQLHRHLLATCPNLIRDRKYHLRLYRQCCSGRELVDGILALGLGVHS\r\nRSQVVGICQVLLDEGALCHVKHDWAFQDRDAQFYRFPGPEPEPVGTHEMEEELA\r\nEAVALLSQRGPDALLTVALRKPPGQRTDEELDLIFEELLHIKAVAHLSNSVKRELAAVLL\r\nFEPHSKAGTVLFSQGDKGTSWYIIWKGSVNVVTHGKGLVTTLHEGDDFGQLALVNDAPRA\r\nATIILREDNCHFLRVDKQDFNRIIKDVEAKTMRLEEHGKVVLVLERASQGAGPSRPPTP\r\nGRNRYTVMSGTPEKILELLLEAMGPDSSAHDPTETFLSDFLLTHRVFMPSAQLCAALLHH\r\nFHVEPAGGSEQERSTYVCNKRQQILRLVSQWVALYGSMLHTDPVATSFLQKLSDLVGRDT\r\nRLSNLLREQWPERRRCHRLENGCGNASPQMKARNLPVWLPNQDEPLPGSSCAIQVGDKVP\r\nYDICRPDHSVLTLQLPVTASVREVMAALAQEDGWTKGQVLVKVNSAGDAIGLQPDARGVA\r\nTSLGLNERLFVVNPQEVHELIPHPDQLGPTVGSAEGLDLVSAKDLAGQLTDHDWSLFNSI\r\nHQVELIHYVLGPQHLRDVTTANLERFMRRFNELQYWVATELCLCPVPGPRAQLLRKFIKL\r\nAAHLKEQKNLNSFFAVMFGLSNSAISRLAHTWERLPHKVRKLYSALERLLDPSWNHRVYR\r\nLALAKLSPPVIPFMPLLLKDMTFIHEGNHTLVENLINFEKMRMMARAARMLHHCRSHNPV\r\nPLSPLRSRVSHLHEDSQVARISTCSEQSLSTRSPASTWAYVQQLKVIDNQRELSRLSREL\r\nEP", "organism": "Homo sapiens", "uniprot_code": "O95398", "uniprot_range_first": 2, "uniprot_range_last": 881, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MKVGWPGESCWQVGLAVEDSPALGAPRVGALPDVVPEGTLLNMVLRRMHRPRSCSYQLLL\nEHQRPSCIQGLRWTPLTNSEESLDFSESLEQASTERVLRAGRQLHRHLLATCPNLIRDRK\nYHLRLYRQCCSGRELVDGILALGLGVHSRSQVVGICQVLLDEGALCHVKHDWAFQDRDAQ\nFYRFPGPEPEPVRTHEMEEELAEAVALLSQRGPDALLTVALRKPPGQRTDEELDLIFEEL\nLHIKAVAHLSNSVKRELAAVLLFEPHSKAGTVLFSQGDKGTSWYIIWKGSVNVVTHGKGL\nVTTLHEGDDFGQLALVNDAPRAATIILREDNCHFLRVDKQDFNRIIKDVEAKTMRLEEHG\nKVVLVLERASQGAGPSRPPTPGRNRYTVMSGTPEKILELLLEAMGPDSSAHDPTETFLSD\nFLLTHRVFMPSAQLCAALLHHFHVEPAGGSEQERSTYVCNKRQQILRLVSQWVALYGSML\nHTDPVATSFLQKLSDLVGRDTRLSNLLREQWPERRRCHRLENGCGNASPQMKARNLPVWL\nPNQDEPLPGSSCAIQVGDKVPYDICRPDHSVLTLQLPVTASVREVMAALAQEDGWTKGQV\nLVKVNSAGDAIGLQPDARGVATSLGLNERLFVVNPQEVHELIPHPDQLGPTVGSAEGLDL\nVSAKDLAGQLTDHDWSLFNSIHQVELIHYVLGPQHLRDVTTANLERFMRRFNELQYWVAT\nELCLCPVPGPRAQLLRKFIKLAAHLKEQKNLNSFFAVMFGLSNSAISRLAHTWERLPHKV\nRKLYSALERLLDPSWNHRVYRLALAKLSPPVIPFMPLLLKDMTFIHEGNHTLVENLINFE\nKMRMMARAARMLHHCRSHNPVPLSPLRSRVSHLHEDSQVARISTCSEQSLSTRSPASTWA\nYVQQLKVIDNQRELSRLSRELEP", "mw": 100.001, "total_mw": 100.001, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "RAS related protein 1b", "short_name": "Rap1b", "sequence": "MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAG\r\nTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDL\r\nEDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEIFYDLVRQINR", "organism": "Mus musculus", "uniprot_code": "Q52L50", "uniprot_range_first": 1, "uniprot_range_last": 167, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAG\nTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDL\nEDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEIFYDLVRQINRKTPVPGKARKKSS\nCQLL", "mw": 18.0, "total_mw": 18.0, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "1mM EDTA, 10mM DTT, 500mM NaCl, 1mM cAMP, and 10mM Tris", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 9.0, "deuteration": null }, "purity_method": null, "name": "Rap guanine nucleotide exchange factor 3 (isoform3) bound to RAS related protein 1b - with cAMP", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Texas, USA", "full_name": "University of Texas Medical Branch", "webpage": "http://www.bmb.utmb.edu/" } ], "contributor_name": "Mark", "contributor_surname": "White", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2013-04-01", "storage_temperature": 10.0, "cell_temperature": 10.0, "exposure_time": 1800.0, "number_of_frames": 5, "wavelength": 0.15418, "sample_detector_distance": 0.489, "concentration_min": 1.0, "concentration_max": 4.0, "sample_volume": null, "flow_rate": null, "s_min": 0.123, "s_max": 6.788, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCS6_fit1_model1_img.png", "software": "SwissModel", "pdb_link": [ { "pdb_code": "3cf6", "ext_code": "3CF6", "ext_type": "pdb", "difference_with_model": "other" } ], "model_title": null, "type_of_model": "atomic", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDCS6_fit1_model1.pdb", "model_mw": 119.4, "bead_radius": 1.9, "log": null, "symmetry": "P1", "comment": "Combined remodelled 3CF6 with 4F7Z and SwissModel", "user": 85 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCS6_fit1_fixed_fit_img.png", "software": "CORAL", "chi_square_value": 0.9, "p_value": 0.0228, "fit_residual_plot": "SASDCS6_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCS6_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/CLcE4b.log", "software_version": "", "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCS6_fit2_model1_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDCS6_fit2_model1.pdb", "model_mw": 120.297, "bead_radius": 3.75, "log": null, "symmetry": "P1", "comment": "SAXNS_DAMMIF", "user": 85 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCS6_fit2_fixed_fit_img.png", "software": "DAMMIF", "chi_square_value": 0.767, "p_value": 0.008, "fit_residual_plot": "SASDCS6_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCS6_fit2.fir", "fit_log": null, "software_version": "", "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "4.6", "i0_calibration_standard": null, "description": null, "experiment_description": "SAXS data from solutions of Rap guanine nucleotide exchange factor 3 (isoform3) bound to RAS related protein 1b - with cAMP - in 1mM EDTA, 10mM DTT, 500mM NaCl, 1mM cAMP, 10mM Tris, pH 9 were collected using a Rigaku BioSAXS-1000 instrument at the Sealy Center For Structural Biology, UTMB-G (Galveston, TX, USA) equipped with a Kratky-2D Rigaku BioSAXS-1000 detector at a sample-detector distance of 0.5 m and at a wavelength of λ = 0.15418 nm (I(s) vs s, where s = 4πsin θ/λ and 2θ is the scattering angle). Solute concentrations ranging between 1 and 4 mg/ml were measured at 10°C. SAXS data were acquired from 5 successive 1800 second frames. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the different curves were scaled for protein concentration to generate the data displayed for this entry.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 119.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 124.0, "porod_mw_error": null, "pddf_i0": 87670.0, "pddf_i0_error": 763.0, "guinier_i0": 85780.0, "guinier_i0_error": 1523.0, "pddf_rg": 4.27, "pddf_rg_error": 0.03, "guinier_rg": 4.05, "guinier_rg_error": 0.09, "pddf_dmax": 14.2, "pddf_dmax_error": null, "porod_volume": 207.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 2, "guinier_point_last": 14, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDCS6_datloglog_img.png", "symmetry": null, "last_modified": "2020-07-03T15:06:29.480452+02:00", "bragg_peak": [] }