{ "code": "SASDCX3", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/A", "project": { "title": "Biophysical investigation of type A PutAs reveals a conserved core oligomeric structure.", "publication": { "title": "Biophysical investigation of type A PutAs reveals a conserved core oligomeric structure.", "author_list": "Korasick DA, Singh H, Pemberton TA, Luo M, Dhatwalia R, Tanner JJ", "journal": "FEBS J", "doi": "10.1111/febs.14165", "pmid": "28710792", "published_date": "2017 Sep" }, "status": "released", "submitted_date": "2017-05-19", "released_date": "2017-07-17" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDCX3.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCX3.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCX3_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCX3_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCX3_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCX3_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCX3.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "MAR 165 CCD", "resolution": null }, "name": "Advanced Light Source (ALS)", "city": "Berkeley, CA", "country": "USA", "beamline_name": "12.3.1 (SIBYLS)", "beam_geometry": "", "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": "DvPutA", "sequence": "MHHHHHHSSGVDLGTENLYFQS\r\nMDQQHLDGKVVERGKEFFRSISGEAPSIFNKGWWTGKVMDWAMQNEDFKVQLFRFVDVLPYLNTSESLLR\r\nHIREYFATEDADIPPVLKWGAGKAGIGGALTAKLMGMTIRSNIEGMARQFIIGDNSKEAVKGLAKLRKDG\r\nFTFTVDLLGEATVSEEESEAYAQGYHEVVDAIAREQEKWKALPGNGPVEGFDWGATPKVNVSIKPSALYS\r\nQAKPVDVEGSVRGILSRLVPIYRKVVAMGGFLCIDMEQLKYKEMTLELFKRLRSDPEFRHYPHLSIVLQA\r\nYLRDTEKDLDDLLHWARSEKLPIGIRLVKGAYWDYETVIAKQNGWEIPVWTDKPESDIAYEKLAHRILEN\r\nSDIVYFACASHNVRTIAAVMETALALNVPEHRYEFQVLYGMAEPVRKGLKNVAGRVRLYCPYGELIPGMA\r\nYLVRRLLENTANESFLRQSFAEGAALERLLENPQKTLHRLLAARPEPRAVEPGPGGLPPFTNDAMIDFTV\r\nPDNRKAFVEALADVRSRFGQTVPLYIGGRDVTTADLIPTTNPAKPAEVVASICQAGRPEIDDAIAAAKKA\r\nALTWRDTSPADRAAYLRRAADICRKRIWELSAWQVVEVGKQWDQAYHDVTEGIDFLEYYAREMLRLGAPR\r\nRMGRAPGEHNHLFYQPKGIAAVIAPWNFPFAIAIGMASAAIVTGNPVIFKPSSISSRIGYNLAEVFREAG\r\nLPEGVFNYCPGRSSIMGDYLVEHPDISLICFTGSMEVGLRIQEKAAKVQPGQRQCKRVIAEMGGKNATII\r\nDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDAIYDRFIERLVKAASSIHIGPSEDPSNYMGPVADA\r\nTLQKNVSDYIRIAEEEGRVLLKRTDLPAEGCYVPLTIVGDIRPEHRIAQEEIFGPVLAVMRAATFDEALS\r\nIANGTRFALTGAVFSRSPEHLDKARREFRVGNLYLNKGSTGALVERQPFGGFAMSGVGSKTGGPDYLLQF\r\nMDPRVVTENTMRRGFTPIDEDDDWIV", "organism": "Desulfovibrio vulgaris", "uniprot_code": "A0A0E0T6R2", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MDQQHLDGKVVERGKEFFRSISGEAPSIFNKGWWTGKVMDWAMQNEDFKVQLFRFVDVLP\nYLNTSESLLRHIREYFATEDADIPPVLKWGAGKAGIGGALTAKLMGMTIRSNIEGMARQF\nIIGDNSKEAVKGLAKLRKDGFTFTVDLLGEATVSEEESEAYAQGYHEVVDAIAREQEKWK\nALPGNGPVEGFDWGATPKVNVSIKPSALYSQAKPVDVEGSVRGILSRLVPIYRKVVAMGG\nFLCIDMEQLKYKEMTLELFKRLRSDPEFRHYPHLSIVLQAYLRDTEKDLDDLLHWARSEK\nLPIGIRLVKGAYWDYETVIAKQNGWEIPVWTDKPESDIAYEKLAHRILENSDIVYFACAS\nHNVRTIAAVMETALALNVPEHRYEFQVLYGMAEPVRKGLKNVAGRVRLYCPYGELIPGMA\nYLVRRLLENTANESFLRQSFAEGAALERLLENPQKTLHRLLAARPEPRAVEPGPGGLPPF\nTNDAMIDFTVPDNRKAFVEALADVRSRFGQTVPLYIGGRDVTTADLIPTTNPAKPAEVVA\nSICQAGRPEIDDAIAAAKKAALTWRDTSPADRAAYLRRAADICRKRIWELSAWQVVEVGK\nQWDQAYHDVTEGIDFLEYYAREMLRLGAPRRMGRAPGEHNHLFYQPKGIAAVIAPWNFPF\nAIAIGMASAAIVTGNPVIFKPSSISSRIGYNLAEVFREAGLPEGVFNYCPGRSSIMGDYL\nVEHPDISLICFTGSMEVGLRIQEKAAKVQPGQRQCKRVIAEMGGKNATIIDDDADLDEAV\nLQVLYSAFGFQGQKCSACSRVIVLDAIYDRFIERLVKAASSIHIGPSEDPSNYMGPVADA\nTLQKNVSDYIRIAEEEGRVLLKRTDLPAEGCYVPLTIVGDIRPEHRIAQEEIFGPVLAVM\nRAATFDEALSIANGTRFALTGAVFSRSPEHLDKARREFRVGNLYLNKGSTGALVERQPFG\nGFAMSGVGSKTGGPDYLLQFMDPRVVTENTMRRGFTPIDEDDDWIV", "mw": 114.496, "total_mw": 228.992, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50 mM Tris-HCl, 50 mM NaCl, 0.5 mM EDTA, and 0.5 mM THP at pH 7.5.", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "Proline utilization A from Desulfovibrio vulgaris 3.0 mg/mL", "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": "John", "contributor_surname": "Tanner", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2012-06-08", "storage_temperature": null, "cell_temperature": null, "exposure_time": null, "number_of_frames": null, "wavelength": null, "sample_detector_distance": null, "concentration_min": null, "concentration_max": 3.0, "sample_volume": null, "flow_rate": null, "s_min": 0.112, "s_max": 3.214, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCX3_fit1_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/SASDCX3_fit1_model1.pdb", "model_mw": 167.0, "bead_radius": 3.4, "log": null, "symmetry": "P2", "comment": "", "user": 166 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCX3_fit1_model2_img.png", "software": "DAMFILT", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "5.0 r6293", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDCX3_fit1_model2.pdb", "model_mw": 167.73, "bead_radius": 4.25, "log": null, "symmetry": "", "comment": "", "user": 166 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCX3_fit1_fixed_fit_img.png", "software": "DAMMIF", "chi_square_value": 1.04, "p_value": 0.0, "fit_residual_plot": "SASDCX3_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCX3_fit1.fir", "fit_log": null, "software_version": "", "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": null, "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from a solution of Proline utilization A from Desulfovibrio vulgaris in 50 mM Tris-HCl, 50 mM NaCl, 0.5 mM EDTA, and 0.5 mM THP at pH 7.5 were collected on the 12.3.1 (SIBYLS) beam line at the Advanced Light Source (ALS; Berkeley, CA, USA) using a MAR 165 CCD detector. One solute concentration of 3 mg/ml was measured. The data were normalized to the intensity of the transmitted beam and radially averaged. The radially averaged scattering of the solvent-blank was subtracted.", "tags": [], "intensity_unit": null, "experimental_mw": 224.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 1625.0, "pddf_i0_error": 6.3, "guinier_i0": 1600.1, "guinier_i0_error": 7.63, "pddf_rg": 4.55, "pddf_rg_error": 0.02, "guinier_rg": 4.37, "guinier_rg_error": 0.03, "pddf_dmax": 16.0, "pddf_dmax_error": null, "porod_volume": 295.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 30, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDCX3_datloglog_img.png", "symmetry": null, "last_modified": "2026-05-18T10:07:00.841981+02:00", "bragg_peak": [] }