{ "code": "SASDEF7", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/nm", "project": { "title": "Structure of the Human TRPML2 Ion Channel Extracytosolic/Lumenal Domain.", "publication": { "title": "Structure of the Human TRPML2 Ion Channel Extracytosolic/Lumenal Domain.", "author_list": "Viet KK, Wagner A, Schwickert K, Hellwig N, Brennich M, Bader N, Schirmeister T, Morgner N, Schindelin H, Hellmich UA", "journal": "Structure", "doi": "10.1016/j.str.2019.04.016", "pmid": "31178222", "published_date": "2019 May 14" }, "status": "released", "submitted_date": "2018-10-30", "released_date": "2019-06-11" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEF7.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEF7.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEF7_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEF7_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEF7_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEF7_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEF7.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": "Transient receptor potential channel mucolipin 2", "short_name": "TRPML2", "sequence": "GLSNQLVVAFKEDNTVAFKHLFLKGYSGTDEDDYSCS\r\nVYTQEDAYESIFFAINQYHQLKDITLGTLGYGENEDNRIGLKVCKQHYKKGTMFPSNETL\r\nNIDNDVELDCVQLDLQDLSKKPPDWKNSSFFRLEFYRLLQVEISFHLKGIDLQTIHSREL\r\nPDCYVFQNTIIFDNKAHSGKIKIYFDSDAKIEECKDLNIFGSTQK", "organism": "Homo sapiens", "uniprot_code": "Q8IZK6", "uniprot_range_first": 1, "uniprot_range_last": 285, "oligomerization": "tetramer", "molecular_type": "protein", "uniprot_sequence": "MARQPYRFPQARIPERGSGVFRLTVRNAMAHRDSEMKEECLREDLKFYFMSPCEKYRARR\nQIPWKLGLQILKIVMVTTQLVRFGLSNQLVVAFKEDNTVAFKHLFLKGYSGTDEDDYSCS\nVYTQEDAYESIFFAINQYHQLKDITLGTLGYGENEDNRIGLKVCKQHYKKGTMFPSNETL\nNIDNDVELDCVQLDLQDLSKKPPDWKNSSFFRLEFYRLLQVEISFHLKGIDLQTIHSREL\nPDCYVFQNTIIFDNKAHSGKIKIYFDSDAKIEECKDLNIFGSTQKNAQYVLVFDAFVIVI\nCLASLILCTRSIVLALRLRKRFLNFFLEKYKRPVCDTDQWEFINGWYVLVIISDLMTIIG\nSILKMEIKAKNLTNYDLCSIFLGTSTLLVWVGVIRYLGYFQAYNVLILTMQASLPKVLRF\nCACAGMIYLGYTFCGWIVLGPYHDKFENLNTVAECLFSLVNGDDMFATFAQIQQKSILVW\nLFSRLYLYSFISLFIYMILSLFIALITDSYDTIKKFQQNGFPETDLQEFLKECSSKEEYQ\nKESSAFLSCICCRRRKRSDDHLIPIS", "mw": 23.354, "total_mw": 93.416, "number_molecules": 4, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "10 mM HEPES pH 6.5 150 mM NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 6.5, "deuteration": null }, "purity_method": null, "name": "Human TRPML2 Ion Channel Extracytosolic/Lumenal Domain at pH 6.5 without Calcium", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "EMBL", "address": "Grenoble, France", "full_name": "European Molecular Biology Laboratory (EMBL) - Grenoble Outstation", "webpage": "https://www.embl.fr/" } ], "contributor_name": "Martha", "contributor_surname": "Brennich", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2018-10-18", "storage_temperature": 20.0, "cell_temperature": 20.0, "exposure_time": 1.0, "number_of_frames": 1200, "wavelength": 0.099, "sample_detector_distance": 2.849, "concentration_min": 0.0, "concentration_max": 0.65, "sample_volume": null, "flow_rate": null, "s_min": 0.035, "s_max": 4.946, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEF7_fit1_model1_img.png", "software": "CORAL", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEF7_fit1_model1.pdb", "model_mw": 92.32, "bead_radius": 1.9, "log": null, "symmetry": null, "comment": null, "user": 119 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/pH65noCaCRP_P1start295_06-1_fit_img.png", "software": "CORAL", "chi_square_value": 1.05, "p_value": 0.37817, "fit_residual_plot": "pH65noCaCRP_P1start295_06-1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEF7_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/pH65noCaCRP_P1start295_06.log", "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEF7_fit2_model1_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEF7_fit2_model1.pdb", "model_mw": 94.1, "bead_radius": 1.8, "log": null, "symmetry": null, "comment": null, "user": 119 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/pH65noCa89_P1_OBLATE_27_fit_img.png", "software": "DAMMIF", "chi_square_value": 1.121, "p_value": 0.354436, "fit_residual_plot": "pH65noCa89_P1_OBLATE_27_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEF7_fit2.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/pH65noCa89_P1_OBLATE_27.log", "software_version": null, "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": "The experimental mass was determined via correlated volume.", "experiment_description": "Synchrotron SAXS data from solutions of Human TRPML2 Ion Channel Extracytosolic/Lumenal Domain 10 mM HEPES pH 6.5 150 mM NaCl, were collected using size exclusion chromatography SAXS (SEC-SAXS) on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.8 m and at a wavelength of λ = 0.099 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). SEC-SAXS was performed at 20°C using the following parameters: Column: Agilent BioSEC 3 bead size 300 μm, Ø 4.6 mm, length 300 mm; Flow rate: 0.3 mL/min; Total acquisition time: 20 min; Injection concentration: 10 mg/mL; Injection volume: 20 μL. The data obtained through the sample elution peak were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the individual subtracted data sets were scaled and averaged to generate the scattering profile displayed in this entry.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 95.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 88.0, "porod_mw_error": null, "pddf_i0": 58.11, "pddf_i0_error": null, "guinier_i0": 58.86, "guinier_i0_error": 0.13, "pddf_rg": 3.361, "pddf_rg_error": null, "guinier_rg": 3.41, "guinier_rg_error": 0.03, "pddf_dmax": 8.9, "pddf_dmax_error": null, "porod_volume": 140.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 10, "guinier_point_last": 73, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDEF7_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }