{ "code": "SASDDQ3", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/A", "project": { "title": "Redox Modulation of Oligomeric State in Proline Utilization A.", "publication": { "title": "Redox Modulation of Oligomeric State in Proline Utilization A.", "author_list": "Korasick DA, Campbell AC, Christgen SL, Chakravarthy S, White TA, Becker DF, Tanner JJ", "journal": "Biophys J", "doi": "10.1016/j.bpj.2018.04.046", "pmid": "29925020", "published_date": "2018 Jun 19" }, "status": "released", "submitted_date": "2018-02-26", "released_date": "2018-06-22" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDQ3.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDQ3.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDQ3_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDQ3_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDQ3_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDQ3_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDQ3.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 100K", "resolution": 172.0 }, "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": "Bifunctional protein PutA", "short_name": "BjPutA", "sequence": ">BjPutA\r\nGHMPNIPPPFTAPYAPDDAEIAARLLPASHLSPPQEARIHRTATRLIEAIRKRDDRLGGVEDMLREFALSTKEGLALMVLAEALLRVPDARTADQFIEDKLGEGDFIHHETKSTAFLVNASAWALGLSARVIQPGETPDGTIGRLVKRLGAPAVRTATRQAMRLMGNHFVLGETIEQALERGKPRSGQKTRYSFDMLGEGARTAADARRYFDAYASAIETIGKAAGNHALPDRPGISVKLSALHPRFEAISRARVMVELVPQLLDLAQRAKAHDLNFTVDAEEADRLELSLDVIAATLADPSLKGWDGFGLAIQAYQKRASAVIDYVDALARAHDRKLMVRLVKGAYWDTEIKRAQERGLDGYPVFTRKAMTDLNYVACASKLLALRPRIFPQFATHNALTVATVLEMAEGSSGFEFQRLHGMGEALYEQLAKDHADIAYRTYAPVGSHRDLLAYLVRRLLENGANSSFVAQAADYRVPVPALLQRPADAIVRPQAAAHPRIPLPCDLFAPERRNSRGVEFGARTALDQLLTDVKAETGDLKPIADATPDQAHAAVAAARAGFAGWSRTPAGIRAAALEQAAHLLESRSAHFIALLQREGGKTLDDALSELREAADFCRYYAAQGRKLFGSETAMPGPTGESNALTMRGRGVFVAISPWNFPLAIFLGQVTAALMAGNSVVAKPAEQTPRIAREAVALLHEAGIPKSALYLVTGDGRIGAALTAHPDIAGVVFTGSTEVARSINRALAAKDGPIVPLIAETGGINAMIADATALPEQVADDVVTSAFRSAGQRCSALRLLFVQEDVADRMIEMVAGAARELKIGDPSDVATHVGPVIDVEAKQRLDAHIARMKTEARLHFAGPAPEGCFVAPHIFELTEAGQLTEEVFGPILHVVRYRPENLERVLRAIERTGYGLTLGVHSRIDDSIEAIIDRVQVGNIYVNRNMIGAVVGVQPFGGNGLSGTGPKAGGPHYLARFATEQTVTINTAAAGGNAALLAGEE", "organism": "Bradyrhizobium diazoefficiens", "uniprot_code": "Q89E26", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "tetramer", "molecular_type": "protein", "uniprot_sequence": "MPNIPPPFTAPYAPDDAEIAARLLPASHLSPPQEARIHRTATRLIEAIRKRDDRLGGVED\nMLREFALSTKEGLALMVLAEALLRVPDARTADQFIEDKLGEGDFIHHETKSTAFLVNASA\nWALGLSARVIQPGETPDGTIGRLVKRLGAPAVRTATRQAMRLMGNHFVLGETIEQALERG\nKPRSGQKTRYSFDMLGEGARTAADARRYFDAYASAIETIGKAAGNHALPDRPGISVKLSA\nLHPRFEAISRARVMVELVPQLLDLAQRAKAHDLNFTVDAEEADRLELSLDVIAATLADPS\nLKGWDGFGLAIQAYQKRASAVIDYVDALARAHDRKLMVRLVKGAYWDTEIKRAQERGLDG\nYPVFTRKAMTDLNYVACASKLLALRPRIFPQFATHNALTVATVLEMAEGSSGFEFQRLHG\nMGEALYEQLAKDHADIAYRTYAPVGSHRDLLAYLVRRLLENGANSSFVAQAADYRVPVPA\nLLQRPADAIVRPQAAAHPRIPLPCDLFAPERRNSRGVEFGARTALDQLLTDVKAETGDLK\nPIADATPDQAHAAVAAARAGFAGWSRTPAGIRAAALEQAAHLLESRSAHFIALLQREGGK\nTLDDALSELREAADFCRYYAAQGRKLFGSETAMPGPTGESNALTMRGRGVFVAISPWNFP\nLAIFLGQVTAALMAGNSVVAKPAEQTPRIAREAVALLHEAGIPKSALYLVTGDGRIGAAL\nTAHPDIAGVVFTGSTEVARSINRALAAKDGPIVPLIAETGGINAMIADATALPEQVADDV\nVTSAFRSAGQRCSALRLLFVQEDVADRMIEMVAGAARELKIGDPSDVATHVGPVIDVEAK\nQRLDAHIARMKTEARLHFAGPAPEGCFVAPHIFELTEAGQLTEEVFGPILHVVRYRPENL\nERVLRAIERTGYGLTLGVHSRIDDSIEAIIDRVQVGNIYVNRNMIGAVVGVQPFGGNGLS\nGTGPKAGGPHYLARFATEQTVTINTAAAGGNAALLAGEE", "mw": 107.558, "total_mw": 430.232, "number_molecules": 4, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50 mM Tris, 50 mM NaCl, 0.5 mM TCEP, 5% (v/v) glycerol", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.8, "deuteration": null }, "purity_method": null, "name": "Proline utilization A from Bradyrhizobium diazoefficiens (formerly Bradyrhizobium japonicum) collected by SEC-SAXS", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "Mizzou", "address": "Columbia, MO, USA", "full_name": "University of Missouri-Columbia", "webpage": "http://missouri.edu/" } ], "contributor_name": "David", "contributor_surname": "Korasick", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2017-07-16", "storage_temperature": null, "cell_temperature": 22.0, "exposure_time": null, "number_of_frames": null, "wavelength": 0.103, "sample_detector_distance": 3.5, "concentration_min": null, "concentration_max": null, "sample_volume": null, "flow_rate": null, "s_min": 0.057, "s_max": 3.832, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDQ3_fit1_model1_img.png", "software": "PDB (Protein Data Bank)", "pdb_link": [ { "pdb_code": "3haz", "ext_code": "3HAZ", "ext_type": "pdb", "difference_with_model": "identical" } ], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDDQ3_fit1_model1.pdb", "model_mw": 424.8, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 290 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDQ3_fit1_fitfoxs_img.png", "software": "FoXS", "chi_square_value": 1.14276, "p_value": 0.0, "fit_residual_plot": "SASDDQ3_fit1_fitfoxsresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDQ3_fit1.dat", "fit_log": null, "software_version": null, "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of proline utilization A from Bradyrhizobium diazoefficiens (formerly Bradyrhizobium japonicum) were collected using SEC-SAXS in 50 mM Tris, 50 mM NaCl, 0.5 mM TCEP, 5% (v/v) glycerol, pH 7.8 on the BioCAT 18ID beam line at the Advanced Photon Source (APS, Argonne, IL, USA) using a Pilatus 100K detector at a sample-detector distance of 3.5 m and at a wavelength of λ = 0.103 nm (l(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). The SEC-SAXS elution was collected at 22°C. 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": 433.8, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 463.2, "pddf_i0_error": null, "guinier_i0": 461.0, "guinier_i0_error": 1.0, "pddf_rg": 5.2, "pddf_rg_error": null, "guinier_rg": 5.22, "guinier_rg_error": 0.02, "pddf_dmax": 14.23, "pddf_dmax_error": null, "porod_volume": 582.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 65, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDDQ3_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }