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.
View the complete summary.json source
{
"code": "SASDBX4",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "Apple Snail Perivitellin Precursor Properties Help Explain Predators' Feeding Behavior.",
"publication": {
"title": "Apple Snail Perivitellin Precursor Properties Help Explain Predators' Feeding Behavior.",
"author_list": "Cadierno MP, Dreon MS, Heras H",
"journal": "Physiol Biochem Zool",
"doi": "10.1086/691526",
"pmid": "28402234",
"published_date": "2017 Jul/Aug"
},
"status": "released",
"submitted_date": "2016-05-29",
"released_date": "2017-04-22"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBX4.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBX4.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBX4_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBX4_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBX4_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBX4_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBX4.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "MAR 165 CCD",
"resolution": null
},
"name": "Brazilian Synchrotron Light Laboratory",
"city": "Campinas",
"country": "Brazil",
"beamline_name": "SAXS2 Beamline",
"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": "Perivitellin-2 31 kDa subunit",
"short_name": "PcPV2-31",
"sequence": "MVKKIHFIMERHASIVAFLLAVLALTESQAFTSVKLPRDEHWPYNYVSIGPAGVWAVNRQNKLFYRTGTY\r\nGDNANMGSGWQFKQDGVGQVDVGKDKVGYINLSGGSLFRIDGISQGNPVGGSPKSWEWWTKYIGMSLRED\r\nTRFSSRIENQNKVLTFTFRTCFWASRITNWCFADSSYTETVTAGGSGTWITKSQLKYKSGTFGNPDTEGG\r\nDWITVDSGSFQHVSSGSGVVLAVRSNGELVKRTGITCSLPQGSGWTSMLNGMSRVDTYGTVAWAVDTYGD\r\nLYFINL",
"organism": "Pomacea canaliculata",
"uniprot_code": "P0C8G7",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "tetramer",
"molecular_type": "protein",
"uniprot_sequence": "MVKKIHFIMERHASIVAFLLAVLALTESQAFTSVKLPRDEHWPYNYVSIGPAGVWAVNRQ\nNKLFYRTGTYGDNANMGSGWQFKQDGVGQVDVGKDKVGYINLSGGSLFRIDGISQGNPVG\nGSPKSWEWWTKYIGMSLREDTRFSSRIENQNKVLTFTFRTCFWASRITNWCFADSSYTET\nVTAGGSGTWITKSQLKYKSGTFGNPDTEGGDWITVDSGSFQHVSSGSGVVLAVRSNGELV\nKRTGITCSLPQGSGWTSMLNGMSRVDTYGTVAWAVDTYGDLYFINL",
"mw": 31.584,
"total_mw": 126.336,
"number_molecules": 4,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Perivitellin-2 67 kDa subunit",
"short_name": "PcPV2-67",
"sequence": "MSQLRWWVVSQLLLLIVVCILDHSEGARVCPKIVPGLDKLRVGVDITKLDLLPLFDLGDNGFRSAVADYT\r\nCDRGQTTVVDGESFDVPDQVDSVVIESSGQQTSSVTTIKSESQISQALSISAGISVDTAKAGFSSSASYA\r\nEMQEAITKYGRTVSQMSAVYTTCSANLSPNLLLGQNPLQTLSRLPSDFTADTEGYYDFIKTYGTHYFNKG\r\nKLGGMFLFTSETDMSYFQNKNSQQVEANIKATFASILSTETGGSSDQSKEVIEFKESSLITAKFFGGRTN\r\nLAADGLTKWQPTIAKLPYFMSGTLSTISSLIADTTKRASMELAVKNYLLKAKVANLDRLTYIRLNSWTVG\r\nHNELRDLSAQLQNLKKKTIFSDEDEKLLQSIEDQVSVPAWFSDRTTFCFRSTAVGSADQCNGQSTSTLCA\r\nEPNRYTQQYMDKTYLGDTGCRLVWKLSTTESSDWFKSVKVNFRWYPTWSPCACGPVGTPFTISAPANSWT\r\nQDYLDVTNPKFGECMLQWMIEVPPTATLWAKNLEFCIDFTCGKKKQCVDANHWTEPYLDISAHEACGMSW\r\nALIAK",
"organism": "Pomacea canaliculata",
"uniprot_code": "P0C8G6",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "tetramer",
"molecular_type": "protein",
"uniprot_sequence": "MSQLRWWVVSQLLLLIVVCILDHSEGARVCPKIVPGLDKLRVGVDITKLDLLPLFDLGDN\nGFRSAVADYTCDRGQTTVVDGESFDVPDQVDSVVIESSGQQTSSVTTIKSESQISQALSI\nSAGISVDTAKAGFSSSASYAEMQEAITKYGRTVSQMSAVYTTCSANLSPNLLLGQNPLQT\nLSRLPSDFTADTEGYYDFIKTYGTHYFNKGKLGGMFLFTSETDMSYFQNKNSQQVEANIK\nATFASILSTETGGSSDQSKEVIEFKESSLITAKFFGGRTNLAADGLTKWQPTIAKLPYFM\nSGTLSTISSLIADTTKRASMELAVKNYLLKAKVANLDRLTYIRLNSWTVGHNELRDLSAQ\nLQNLKKKTIFSDEDEKLLQSIEDQVSVPAWFSDRTTFCFRSTAVGSADQCNGQSTSTLCA\nEPNRYTQQYMDKTYLGDTGCRLVWKLSTTESSDWFKSVKVNFRWYPTWSPCACGPVGTPF\nTISAPANSWTQDYLDVTNPKFGECMLQWMIEVPPTATLWAKNLEFCIDFTCGKKKQCVDA\nNHWTEPYLDISAHEACGMSWALIAK",
"mw": 62.517,
"total_mw": 250.068,
"number_molecules": 4,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Tris-HCl",
"concentration_unit": "mM",
"comment": null,
"additive": null,
"concentration": 20.0,
"pka": null,
"ph": 8.5,
"deuteration": null
},
"purity_method": null,
"name": "Albumen gland precursor of perivitellin-2 (PcPV2)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [],
"contributor_name": "Marcos",
"contributor_surname": "Dreon",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2014-06-10",
"storage_temperature": 25.0,
"cell_temperature": 25.0,
"exposure_time": 300.0,
"number_of_frames": 5,
"wavelength": null,
"sample_detector_distance": null,
"concentration_min": 0.6,
"concentration_max": 2.4,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.085,
"s_max": 2.081,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBX4_fit1_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "r3695",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBX4_fit1_model1.pdb",
"model_mw": 191.5,
"bead_radius": 3.6,
"log": null,
"symmetry": "",
"comment": "",
"user": 128
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBX4_fit1_fit_img.png",
"software": null,
"chi_square_value": 1.76,
"p_value": 0.0,
"fit_residual_plot": "SASDBX4_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBX4_fit1.fir",
"fit_log": null,
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBX4_fit2_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "r3695",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBX4_fit2_model1.pdb",
"model_mw": 191.5,
"bead_radius": 3.6,
"log": null,
"symmetry": "",
"comment": "",
"user": 128
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBX4_fit2_fit_img.png",
"software": null,
"chi_square_value": 1.735,
"p_value": 0.0,
"fit_residual_plot": "SASDBX4_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBX4_fit2.fir",
"fit_log": null,
"software_version": null,
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": null,
"experiment_description": "X-ray synchrotron radiation scattering data from solutions of the albumen gland precursor of perivitellin-2 (PcPV2) in 20 mM Tris-HCl, pH 8.5 on the D02A-SAXS2 Beamline at the Laboratorio Nacional de Luz Sincrotron (LNLS, Campinas, Brazil) using a MAR Image Plate detector (I(s) vs s, where s = 4π sin θ/λ, 2θ is the scattering angle and λ the X-ray wavelength, 0.155 nm). Different solute concentrations in the range 0.60-2.40 mg/ml were measured. Five successive 300 second frames were collected. 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. The low angle data collected were obtained from a single concentration scattering curve. PcPV2 is an oligomeric protein of 400kDa composed of the perivitellin-2 31 kDa and perivitellin-2 67 kDa subunits.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 400.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 0.0004835,
"pddf_i0_error": null,
"guinier_i0": 0.00049,
"guinier_i0_error": null,
"pddf_rg": 4.86,
"pddf_rg_error": 0.009,
"guinier_rg": 4.84,
"guinier_rg_error": 0.18,
"pddf_dmax": 16.96,
"pddf_dmax_error": null,
"porod_volume": 294.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 3,
"guinier_point_last": 20,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDBX4_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
