The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
Every source field is expanded here, including empty values, list members and fields already shown above.
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{
"code": "SASDDP3",
"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/SASDDP3.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDP3.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDP3_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDP3_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDP3_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDP3_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDP3.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": "dimer",
"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": 215.116,
"number_molecules": 2,
"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": "N-propargyl glycine-Inactivated 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": 3.826,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDP3_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/SASDDP3_fit1_model1.pdb",
"model_mw": 212.4,
"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/SASDDP3_fit1_fitfoxs_img.png",
"software": "FoXS",
"chi_square_value": 2.981613,
"p_value": 0.0,
"fit_residual_plot": "SASDDP3_fit1_fitfoxsresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDP3_fit1.dat",
"fit_log": null,
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDP3_fit2_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDP3_fit2_model1.pdb",
"model_mw": 212.4,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 290
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDP3_fit2_model2_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDP3_fit2_model2.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/SASDDP3_fit2_fitfoxs_img.png",
"software": "MultiFoXS",
"chi_square_value": 1.649088,
"p_value": 0.0,
"fit_residual_plot": "SASDDP3_fit2_fitfoxsresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDP3_fit2.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 N-propargyl glycine-Inactivated 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": 249.7,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 380.4,
"pddf_i0_error": null,
"guinier_i0": 377.5,
"guinier_i0_error": 0.9,
"pddf_rg": 4.7,
"pddf_rg_error": null,
"guinier_rg": 4.63,
"guinier_rg_error": 0.02,
"pddf_dmax": 14.42,
"pddf_dmax_error": null,
"porod_volume": 324.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 76,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDDP3_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
