{ "code": "SASDAF7", "status": "Published", "type_of_curve": "Merged", "angular_unit": "1/nm", "project": { "title": "Distinctive features and structural significance of the Homo sapiens ethylmalonic encephalopathy protein iron binding site", "publication": null, "status": "released", "submitted_date": "2015-02-17", "released_date": "2017-02-08" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDAF7.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDAF7.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAF7_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAF7_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDAF7_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAF7_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDAF7.sascif", "experiment": { "instrument": { "detector": { "type": "Custom-built", "name": "Pilatus 1M-W", "resolution": 0.172 }, "name": "DORIS III, DESY", "city": "Hamburg", "country": "Germany", "beamline_name": "EMBL X33", "beam_geometry": "0.60", "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": "Persulfide dioxygenase ETHE1, mitochondrial", "short_name": "hETHE1", "sequence": null, "organism": "Homo sapiens", "uniprot_code": "O95571", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MAEAVLRVARRQLSQRGGSGAPILLRQMFEPVSCTFTYLLGDRESREAVLIDPVLETAPR\nDAQLIKELGLRLLYAVNTHCHADHITGSGLLRSLLPGCQSVISRLSGAQADLHIEDGDSI\nRFGRFALETRASPGHTPGCVTFVLNDHSMAFTGDALLIRGCGRTDFQQGCAKTLYHSVHE\nKIFTLPGDCLIYPAHDYHGFTVSTVEEERTLNPRLTLSCEEFVKIMGNLNLPKPQQIDFA\nVPANMRCGVQTPTA", "mw": 27.873, "total_mw": 55.746, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50 mM Tris 150 mM NaCl 2 mM TCEP", "concentration_unit": "mM", "comment": "TCEP does not reduce metals in solution, but prevents aggregation and precipitation of the protein", "additive": "150 mM NaCl\r\n2 mM TCEP", "concentration": 50.0, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "Metal-bound hETHE1", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "EMBL-Hamburg", "address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany", "full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation", "webpage": "http://www.embl-hamburg.de/index.php" } ], "contributor_name": "Al", "contributor_surname": "Kikhney", "orcid": "https://orcid.org/0000-0003-1321-3956" }, { "affiliation": [ { "short_name": null, "address": "Bolzano, Italy", "full_name": "Libera Università di Bozen-Bolzano", "webpage": "https://www.unibz.it/" } ], "contributor_name": "Marco", "contributor_surname": "Salomone-Stagni", "orcid": null } ], "concentration_method": null, "concentration_unit": "mg/ml", "date": "2007-10-21", "storage_temperature": null, "cell_temperature": 9.0, "exposure_time": 30.0, "number_of_frames": 4, "wavelength": 0.15, "sample_detector_distance": 2.7, "concentration_min": 2.0, "concentration_max": 5.0, "sample_volume": null, "flow_rate": null, "s_min": 0.083, "s_max": 4.981, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDAF7_fit1_model1_img.png", "software": "DAMMIN", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "5.3", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDAF7_fit1_model1.pdb", "model_mw": 39.435, "bead_radius": 1.8, "log": "https://www.sasbdb.org/media/log_files/P03-N-P2.log", "symmetry": "P2", "comment": "", "user": 4 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAF7_fit1_fixed_fit_img.png", "software": "DAMMIN", "chi_square_value": 1.308, "p_value": 0.0026, "fit_residual_plot": "SASDAF7_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDAF7_fit1.fir", "fit_log": null, "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDAF7_fit2_model1_img.png", "software": "PDB (Protein Data Bank)", "pdb_link": [ { "pdb_code": "4chl", "ext_code": "4CHL", "ext_type": "pdb", "difference_with_model": null } ], "model_title": null, "type_of_model": "atomic", "software_version": "2.8.3", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDAF7_fit2_model1.pdb", "model_mw": 51.4, "bead_radius": null, "log": "https://www.sasbdb.org/media/log_files/4CHL01.log", "symmetry": "", "comment": "", "user": 4 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAF7_fit2_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 1.35, "p_value": 0.0615, "fit_residual_plot": "SASDAF7_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDAF7_fit2.fit", "fit_log": null, "software_version": "2", "description": "" } ], "estimated_volume_method": "DAMMIN", "pddf_software": "ATSAS GNOM", "pddf_software_version": "GNOM 5.0", "i0_calibration_standard": null, "description": "Metal-bound hETHE1 was shown by SAXS to be a globular protein compatible with a dimeric hETHE1 in solution. The calculated scattering pattern from a high resolution model of dimeric ETHE1 is in a very good agreement (χ2 value of 1.5) with the experimental data from hETHE1. The low resolution shape of metal-bound hETHE1 was reconstructed ab initio using DAMMIN with P2 symmetry imposed. The ab initio model fits the experimental data with a discrepancy χ2 = 1.3 and is in a good agreement with the high resolution ETHE1 structure.", "experiment_description": null, "tags": [ "X33" ], "intensity_unit": null, "experimental_mw": 42.0, "experimental_mw_error": 4.0, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 42.0, "porod_mw_error": 4.0, "pddf_i0": 98.52, "pddf_i0_error": 0.1952, "guinier_i0": 99.96, "guinier_i0_error": 0.29, "pddf_rg": 2.408, "pddf_rg_error": 0.004, "guinier_rg": 2.47, "guinier_rg_error": 0.24, "pddf_dmax": 7.5, "pddf_dmax_error": 1.0, "porod_volume": 70.0, "porod_volume_error": 7.0, "estimated_volume": 78.87, "estimated_volume_error": null, "guinier_point_first": 32, "guinier_point_last": 293, "pddf_point_first": 32, "pddf_point_last": 1400, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDAF7_datloglog_img.png", "symmetry": null, "last_modified": "2023-05-25T11:21:52.654103+02:00", "bragg_peak": [] }