{ "code": "SASDEW8", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/nm", "project": { "title": "Interaction of the GTPase Elongation Factor Like-1 with the Shwachman-Diamond Syndrome Protein and Its Missense Mutations.", "publication": { "title": "Interaction of the GTPase Elongation Factor Like-1 with the Shwachman-Diamond Syndrome Protein and Its Missense Mutations.", "author_list": "Gijsbers A, Montagut DC, Méndez-Godoy A, Altamura D, Saviano M, Siliqi D, Sánchez-Puig N", "journal": "Int J Mol Sci", "doi": "10.3390/ijms19124012", "pmid": "30545121", "published_date": "2018 Dec 12" }, "status": "released", "submitted_date": "2018-12-06", "released_date": "2018-12-14" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEW8.dat", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEW8.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEW8_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEW8_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEW8_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEW8_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEW8.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 2M", "resolution": null }, "name": "PETRA III", "city": "DESY; Hamburg", "country": "Germany", "beamline_name": "EMBL P12", "beam_geometry": null, "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": "Ribosome maturation protein SDO1", "short_name": "SDO1_12", "sequence": "LSEKERQLMLNKVNNEMLTIVSAKCINPVSKKRYPPTMIHKALQELKFSPVINKPAKLQA\r\n LEAIKLLVSKQIIPIVRAKMKVKVAISEPSRQPELIEKISKLIASSPGESTKPELDPWTC\r\n TGLIDPVNYRDLMTLCDKKGTVQVLDMAVIDNTTHN", "organism": "Saccharomyces cerevisiae", "uniprot_code": "Q07953", "uniprot_range_first": 1, "uniprot_range_last": 250, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MPINQPSGQIKLTNVSLVRLKKARKRFEVACYQNKVQDYRKGIEKDLDEVLQIHQVFMNV\nSKGLVANKEDLQKCFGTTNVDDVIEEIMHKGEIQLSEKERQLMLNKVNNEMLTIVSAKCI\nNPVSKKRYPPTMIHKALQELKFSPVINKPAKLQALEAIKLLVSKQIIPIVRAKMKVKVAI\nSEPSRQPELIEKISKLIASSPGESTKPELDPWTCTGLIDPVNYRDLMTLCDKKGTVQVLD\nMAVIDNTTHN", "mw": 17.47, "total_mw": 17.47, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50 mM Tris pH 8.0, 10% glycerol, 300 mM NaCl, 5 mM MgCl2.", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": null, "deuteration": null }, "purity_method": null, "name": "Shwachman-Bodian-Diamond Syndrome protein (SDO1) with domains 2 and 3", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Bari, Italy", "full_name": "CNR - Institute of Crystallography, Bari, Italy", "webpage": "http://www.ba.ic.cnr.it" } ], "contributor_name": "Dritan", "contributor_surname": "Siliqi", "orcid": "https://orcid.org/0000-0003-1415-8725" } ], "concentration_method": null, "concentration_unit": null, "date": "2015-08-14", "storage_temperature": null, "cell_temperature": 20.0, "exposure_time": 1.0, "number_of_frames": 1850, "wavelength": 0.124, "sample_detector_distance": 3.0, "concentration_min": null, "concentration_max": 15.0, "sample_volume": null, "flow_rate": null, "s_min": 0.136, "s_max": 4.249, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEW8_fit1_model1_img.png", "software": "DAMFILT", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "DAMFILT 5.", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEW8_fit1_model1.pdb", "model_mw": 15.548, "bead_radius": 1.75, "log": null, "symmetry": null, "comment": null, "user": 396 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/d1d2d3_8_fit_img.png", "software": "DAMMIF", "chi_square_value": 1.279, "p_value": 0.043129, "fit_residual_plot": "d1d2d3_8_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEW8_fit1.fir", "fit_log": null, "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEW8_fit2_model1_img.png", "software": "MultiFoXS", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEW8_fit2_model1.pdb", "model_mw": 17.48, "bead_radius": null, "log": null, "symmetry": null, "comment": "The model is obtained by MultiFOXs. The protein is described by one state", "user": 396 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/multi_state_model_1_1_1_8ztSovl_fit_img.png", "software": "CRYSOL", "chi_square_value": 1.343658, "p_value": 0.035591, "fit_residual_plot": "multi_state_model_1_1_1_8ztSovl_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEW8_fit2.fit", "fit_log": null, "software_version": null, "description": "" } ], "estimated_volume_method": null, "pddf_software": "ScÅtter", "pddf_software_version": "3.1v", "i0_calibration_standard": null, "description": "SEC-SAXS (using FPLC–Malvern TDA system ) was performed at 20°C using the following parameters: Column: Superdex 200 Increase 10/300GL ; Flow rate: 0.4 mL/min; Total acquisition time: 1850s; Sample injection concentration: 15 mg/mL; Injection volume: 50μL.", "experiment_description": "Synchrotron SAXS data from solutions of Shwachman-Bodian-Diamond Syndrome protein (SDO1) with domains 2 and 3 in 50 mM Tris pH 8.0, 10% glycerol, 300 mM NaCl and 5 mM MgCl2, pH 8 were collected on the EMBL P12 beam line at the PETRA III storage ring (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). The data obtained through the sample elution peak (collected as successive 1 second frames) 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": null, "experimental_mw": 18.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 16.0, "porod_mw_error": null, "pddf_i0": 1109.0, "pddf_i0_error": 17.6, "guinier_i0": 1181.87, "guinier_i0_error": 2.26, "pddf_rg": 1.96, "pddf_rg_error": 0.002, "guinier_rg": 2.05, "guinier_rg_error": 0.013, "pddf_dmax": 6.2, "pddf_dmax_error": null, "porod_volume": 25.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 7, "guinier_point_last": 190, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDEW8_datloglog_img.png", "symmetry": null, "last_modified": "2024-07-15T11:06:06.222393+02:00", "bragg_peak": [] }