{ "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": [] }