{ "code": "SASDES5", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/nm", "project": { "title": "Structural characterization of the third scavenger receptor cysteine-rich domain of murine neurotrypsin.", "publication": { "title": "Structural characterization of the third scavenger receptor cysteine-rich domain of murine neurotrypsin.", "author_list": "Canciani A, Catucci G, Forneris F", "journal": "Protein Sci", "doi": "10.1002/pro.3587", "pmid": "30748049", "published_date": "2019 Apr" }, "status": "released", "submitted_date": "2018-10-03", "released_date": "2019-02-13" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDES5.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDES5.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDES5_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDES5_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDES5_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDES5_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDES5.sascif", "experiment": { "instrument": { "detector": { "type": "Dectris", "name": "Pilatus 1M", "resolution": 172.0 }, "name": "ESRF", "city": "Grenoble", "country": "France", "beamline_name": "BM29", "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": "Mouse Neurotrypsin Scavenger Receptor Cysteine-Rich Domain 3", "short_name": "mmNT-SRCR3", "sequence": "GTGEFTSGSGFPIRLVDGENKKEGRVEVFVNGQWGTICDDGWTDKHAAVICRQLGYKGPARARTMAYFGEGKGPIHMDNVKCTGNEKALADCVKQDIGRHNCRHSEDAGVICDYLEKKASS", "organism": "Mus musculus", "uniprot_code": "O08762", "uniprot_range_first": 383, "uniprot_range_last": 494, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MALARCVLAVILGALSVVARADPVSRSPLHRPHPSPPRSQHAHYLPSSRRPPRTPRFPLP\nLRIPAAQRPQVLSTGHTPPTIPRRCGAGESWGNATNLGVPCLHWDEVPPFLERSPPASWA\nELRGQPHNFCRSPDGSGRPWCFYRNAQGKVDWGYCDCGQGPALPVIRLVGGNSGHEGRVE\nLYHAGQWGTICDDQWDNADADVICRQLGLSGIAKAWHQAHFGEGSGPILLDEVRCTGNEL\nSIEQCPKSSWGEHNCGHKEDAGVSCVPLTDGVIRLAGGKSTHEGRLEVYYKGQWGTVCDD\nGWTEMNTYVACRLLGFKYGKQSSVNHFDGSNRPIWLDDVSCSGKEVSFIQCSRRQWGRHD\nCSHREDVGLTCYPDSDGHRLSPGFPIRLVDGENKKEGRVEVFVNGQWGTICDDGWTDKHA\nAVICRQLGYKGPARARTMAYFGEGKGPIHMDNVKCTGNEKALADCVKQDIGRHNCRHSED\nAGVICDYLEKKASSSGNKEMLSSGCGLRLLHRRQKRIIGGNNSLRGAWPWQASLRLRSAH\nGDGRLLCGATLLSSCWVLTAAHCFKRYGNNSRSYAVRVGDYHTLVPEEFEQEIGVQQIVI\nHRNYRPDRSDYDIALVRLQGPGEQCARLSTHVLPACLPLWRERPQKTASNCHITGWGDTG\nRAYSRTLQQAAVPLLPKRFCKERYKGLFTGRMLCAGNLQEDNRVDSCQGDSGGPLMCEKP\nDESWVVYGVTSWGYGCGVKDTPGVYTRVPAFVPWIKSVTSL", "mw": 13.165, "total_mw": 13.165, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "25 mM HEPES, 0.1 M NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "Neurotrypsin Scavenger Receptor Cysteine-Rich Domain 3 (mmNT-SRCR3) - from SEC-SAXS", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Italy", "full_name": "University of Pavia", "webpage": "http://wcm-3.unipv.it" } ], "contributor_name": "Federico", "contributor_surname": "Forneris", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2017-05-20", "storage_temperature": 20.0, "cell_temperature": 20.0, "exposure_time": 1.0, "number_of_frames": 22, "wavelength": 0.09919, "sample_detector_distance": 2.87, "concentration_min": null, "concentration_max": 15.0, "sample_volume": null, "flow_rate": null, "s_min": 0.033, "s_max": 4.944, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDES5_fit1_model1_img.png", "software": "PDB (Protein Data Bank)", "pdb_link": [ { "pdb_code": "6h8m", "ext_code": "6H8M", "ext_type": "pdb", "difference_with_model": "derived" } ], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDES5_fit1_model1.pdb", "model_mw": 11.82, "bead_radius": null, "log": null, "symmetry": null, "comment": "Model generated from PDB file by selecting only chain A", "user": 294 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/A00_fit_img.png", "software": "CRYSOL", "chi_square_value": 1.399, "p_value": 0.0, "fit_residual_plot": null, "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDES5_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/A00.log", "software_version": "2.8.3", "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "2.8.4", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data, I(s) vs s (where s = 4πsinθ/λ, 2θ is the scattering angle and λ the X-ray wavelength), were collected from a sample of mmNT-SRCR3 using continuous-flow size-exclusion chromatography SAXS (SEC-SAXS) on the BM29 beam line of the ESRF (Grenoble France) coupled to a Nexera High Pressure Liquid/Chromatography (HPLC; Shimadzu) system. Data were collected using a Pilatus 1M detector at a sample-detector distance of 2.87 m (s-range; 0.03–4.5 nm-1) at a wavelength of λ = 0.09919 nm (12.5 keV). The SEC mobile phase consisted of 25 mM HEPES/NaOH, 0.1 M NaCl, pH 8, (20°C). The protein was concentrated to 15 mg/mL and a 15 µL of sample was run on a Superdex 75 Increase 3.2/300 column (GE Healthcare). Analysis and of the scattering intensities measured from the SEC-elution sample peak (22 successive 1 s frames) and the subtraction of intensities measured from an appropriate solvent-blank were was performed using CHROMIXS of the ATSAS suite. Comparison of in-solution scattering to crystallographic data was carried out with CRYSOL.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 12.0, "experimental_mw_error": null, "guinier_i0_mw": 11.99, "guinier_i0_mw_error": 1.0, "porod_mw": 11.5, "porod_mw_error": null, "pddf_i0": 13.45, "pddf_i0_error": 0.019, "guinier_i0": 13.48, "guinier_i0_error": 0.015, "pddf_rg": 1.53, "pddf_rg_error": 0.003, "guinier_rg": 1.54, "guinier_rg_error": 0.03, "pddf_dmax": 4.54, "pddf_dmax_error": 0.02, "porod_volume": 23.85, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 27, "guinier_point_last": 173, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDES5_datloglog_img.png", "symmetry": null, "last_modified": "2024-06-23T13:31:55.412859+02:00", "bragg_peak": [] }