{ "code": "SASDBW4", "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/SASDBW4.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBW4.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBW4_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBW4_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBW4_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBW4_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBW4.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 ovorubin-1", "short_name": "Ovo1", "sequence": "MFVATSLLLAIATLVVRASPHNYLIMDIEPPKSVSERDILNLLSPLQVKHSFRVTGSTRL\r\nLIVIRLDAQSYEKLDEITVPGKVEVIPAVNMADTMERCGVSWPRVELTDDNVTLFESEST\r\nLTDVTKEQLKAMLIGYGEHMSGLLQAHRFEYYQAAGATPHRHFVFVNSVPDEIEVFGREG\r\nVDIWGGPGEFVVKPQYVTRI", "organism": "Pomacea canaliculata", "uniprot_code": "J7I2T6", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "unknown", "molecular_type": "protein", "uniprot_sequence": "MFVATSLLLAIATLVVRASPHNYLIMDIEPPKSVSERDILNLLSPLQVKHSFRVTGSTRL\nLIVIRLDAQSYEKLDEITVPGKVEVIPAVNMADTMERCGVSWPRVELTDDNVTLFESEST\nLTDVTKEQLKAMLIGYGEHMSGLLQAHRFEYYQAAGATPHRHFVFVNSVPDEIEVFGREG\nVDIWGGPGEFVVKPQYVTRI", "mw": 22.384, "total_mw": 22.384, "number_molecules": 0, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "Perivitellin ovorubin-2", "short_name": "Ovo2", "sequence": "MAEHRIPVLLLLVVVAASSLAQQIPLQKHYIIYEVRNIEKTPEEVKEEMKDTDILYSFKA\r\nLGAPSYHIVVEVNPRNMRKLEEVELKGKIRMVPVVNMVDVAETLGVSWPRSGARLLDVNL\r\nTLIERTLNQEGLTSQESEAHLKGFMEELKDRLQQYNYQAFFTIGASPPKMYIYINIPYEE\r\nVDKFACIGINQFGGPAAVNTTVSFISSFPK", "organism": "Pomacea canaliculata", "uniprot_code": "J7HZ90", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "unknown", "molecular_type": "protein", "uniprot_sequence": "MAEHRIPVLLLLVVVAASSLAQQIPLQKHYIIYEVRNIEKTPEEVKEEMKDTDILYSFKA\nLGAPSYHIVVEVNPRNMRKLEEVELKGKIRMVPVVNMVDVAETLGVSWPRSGARLLDVNL\nTLIERTLNQEGLTSQESEAHLKGFMEELKDRLQQYNYQAFFTIGASPPKMYIYINIPYEE\nVDKFACIGINQFGGPAAVNTTVSFISSFPK", "mw": 23.801, "total_mw": 23.801, "number_molecules": 0, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "Perivitellin ovorubin-3", "short_name": "Ovo3", "sequence": "MYALAIALLAFSTFVSNAFANKEYLLLDIRDATTSEIISALRDVEIELKVKAKGIARHLI\r\nVVKQNDANLQKLGEIDIPGRSCSTPVEDLDNLMEDIGISWPRNELTSVNVTLFERTLDLK\r\nDKTMEQFWSEAKAYGQLVKPVLSSFTYRAFKANGAYPPKVYFFVNLPRENLNDASSKGID\r\nIFGGPGKARTTVQYISVCVAVSHSTFSCRQSVGDMKCMFQQPPVPARSSGRPGRYDNQVR\r\nHGVRIAAPVMENFPNYILLSKGTFPPKSRFRSNLWGLVNGSRRISRRGKPLLHNKHPNHY\r\nQMELKYTIATH", "organism": "Pomacea canaliculata", "uniprot_code": "J7I5Z5", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "unknown", "molecular_type": "protein", "uniprot_sequence": "MYALAIALLAFSTFVSNAFANKEYLLLDIRDATTSEIISALRDVEIELKVKAKGIARHLI\nVVKQNDANLQKLGEIDIPGRSCSTPVEDLDNLMEDIGISWPRNELTSVNVTLFERTLDLK\nDKTMEQFWSEAKAYGQLVKPVLSSFTYRAFKANGAYPPKVYFFVNLPRENLNDASSKGID\nIFGGPGKARTTVQYISVCVAVSHSTFSCRQSVGDMKCMFQQPPVPARSSGRPGRYDNQVR\nHGVRIAAPVMENFPNYILLSKGTFPPKSRFRSNLWGLVNGSRRISRRGKPLLHNKHPNHY\nQMELKYTIATH", "mw": 34.957, "total_mw": 34.957, "number_molecules": 0, "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 ovorubin (lipoglycocarotenoprotein agPcOvo: an oligomeric protein)", "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": "mg/ml", "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": 1.04, "concentration_max": 4.16, "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/SASDBW4_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/SASDBW4_fit1_model1.pdb", "model_mw": 275.0, "bead_radius": 3.1, "log": null, "symmetry": "", "comment": "", "user": 128 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBW4_fit1_fit_img.png", "software": null, "chi_square_value": 1.641, "p_value": 2.4e-05, "fit_residual_plot": "SASDBW4_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBW4_fit1.fir", "fit_log": null, "software_version": null, "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBW4_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/SASDBW4_fit2_model1.pdb", "model_mw": 275.5, "bead_radius": 3.1, "log": null, "symmetry": "", "comment": "", "user": 128 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBW4_fit2_fit_img.png", "software": null, "chi_square_value": 1.625, "p_value": 2.4e-05, "fit_residual_plot": "SASDBW4_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBW4_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": "agPcOvo is an oligomeric lipoglycocarotenoprotein isolated from the albumen gland of P. canaliculata that consists of different perivitellin ovorubin subunits (Ovo1-3) that form a complex with a molecular weight of 300 kDa.", "experiment_description": "X-ray synchrotron radiation scattering data from a solution of the ovorubin albumen gland precursor in 20 mM Tris-HCl, pH 8.5 were collected 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 1.04-4.16 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.", "tags": [], "intensity_unit": null, "experimental_mw": 300.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 0.001091, "pddf_i0_error": null, "guinier_i0": 0.0011, "guinier_i0_error": null, "pddf_rg": 4.27, "pddf_rg_error": 0.003, "guinier_rg": 4.26, "guinier_rg_error": 0.01, "pddf_dmax": 14.94, "pddf_dmax_error": null, "porod_volume": 526.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 6, "guinier_point_last": 24, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDBW4_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }