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{
"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": []
}
