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{
"code": "SASDD33",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "An NAD<sup>+</sup> Phosphorylase Toxin Triggers Mycobacterium tuberculosis Cell Death.",
"publication": {
"title": "An NAD<sup>+</sup> Phosphorylase Toxin Triggers Mycobacterium tuberculosis Cell Death.",
"author_list": "Freire DM, Gutierrez C, Garza-Garcia A, Grabowska AD, Sala AJ, Ariyachaokun K, Panikova T, Beckham KSH, Colom A, Pogenberg V, Cianci M, Tuukkanen A, Boudehen YM, Peixoto A, Botella L, Svergun DI, Schnappinger D, Schneider TR, Genevaux P, de Carvalho LPS, Wilmanns M, Parret AHA, Neyrolles O",
"journal": "Mol Cell",
"doi": "10.1016/j.molcel.2019.01.028",
"pmid": "30792174",
"published_date": "2019 Feb 8"
},
"status": "released",
"submitted_date": "2018-01-12",
"released_date": "2019-02-25"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDD33.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDD33.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD33_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD33_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDD33_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD33_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDD33.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": "Mycobacterial cidal toxin",
"short_name": "MbcT",
"sequence": "VSDALDEGLVQRIDARGTIEWSETCYRYTGAHRDALSGEGARRFGGRWNPPLLFPAIYLADSAQACMVEVERAAQAASTTAEKMLEAAYRLHTIDVTDLAVLDLTTPQAREAVGLENDDIYGDDWSGCQAVGHAAWFLHMQGVLVPAAGGVGLVVTAYEQRTRPGQLQLRQSVDLTPALYQELRAT",
"organism": "Mycobacterium tuberculosis",
"uniprot_code": "P9WLP9",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "hexamer",
"molecular_type": "protein",
"uniprot_sequence": "MSDALDEGLVQRIDARGTIEWSETCYRYTGAHRDALSGEGARRFGGRWNPPLLFPAIYLA\nDSAQACMVEVERAAQAASTTAEKMLEAAYRLHTIDVTDLAVLDLTTPQAREAVGLENDDI\nYGDDWSGCQAVGHAAWFLHMQGVLVPAAGGVGLVVTAYEQRTRPGQLQLRQSVDLTPALY\nQELRAT",
"mw": 20.248,
"total_mw": 121.488,
"number_molecules": 6,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Mycobacterial cidal antitoxin",
"short_name": "MbcA",
"sequence": "GAMGVNVLASTVSGAIERLGLTYEEVGDIVDASPRSVARWTAGQVVPQRLNKQRLIELAYVADALAEVLPRDQANVWMFSPNRLLEHRKPADLVRDGEYQRVLALIDAMAEGVFV",
"organism": "Mycobacterium tuberculosis",
"uniprot_code": "P9WLP7",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "hexamer",
"molecular_type": "protein",
"uniprot_sequence": "MGVNVLASTVSGAIERLGLTYEEVGDIVDASPRSVARWTAGQVVPQRLNKQRLIELAYVA\nDALAEVLPRDQANVWMFSPNRLLEHRKPADLVRDGEYQRVLALIDAMAEGVFV",
"mw": 12.616,
"total_mw": 75.696,
"number_molecules": 6,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "100 mM HEPES, 100 mM NaCl",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Toxin/Antitoxin complex from M. tuberculosis",
"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": "Anne",
"contributor_surname": "Tuukkanen",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2015-06-02",
"storage_temperature": 20.0,
"cell_temperature": 10.0,
"exposure_time": 0.05,
"number_of_frames": 20,
"wavelength": 0.124,
"sample_detector_distance": 3.0,
"concentration_min": null,
"concentration_max": 0.63,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.098,
"s_max": 4.801,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD33_fit1_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "6fkg",
"ext_code": "6FKG",
"ext_type": "pdb",
"difference_with_model": "pdb"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDD33_fit1_model1.pdb",
"model_mw": 191.7,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 27
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD33_fit1_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.007,
"p_value": 0.259841,
"fit_residual_plot": "SASDD33_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDD33_fit1.fit",
"fit_log": null,
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD33_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/SASDD33_fit2_model1.pdb",
"model_mw": 142.575,
"bead_radius": 2.5,
"log": null,
"symmetry": "P1",
"comment": null,
"user": 27
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD33_fit2_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 1.062,
"p_value": 0.080559,
"fit_residual_plot": "SASDD33_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDD33_fit2.fir",
"fit_log": null,
"software_version": null,
"description": null
}
],
"estimated_volume_method": "DAMMIF",
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of the M. tuberculosis suicide toxin/antitoxin complex in 100 mM HEPES, 100 mM NaCl, pH 7.5 were collected on the EMBL bioSAXS P12 beam line at the PETRA III storage ring (DESY, 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). One solute concentration of 0.63 mg/ml was measured at 10°C. 20 successive 0.050 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 154.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 154.0,
"porod_mw_error": null,
"pddf_i0": 31320.0,
"pddf_i0_error": 114.0,
"guinier_i0": 31335.6,
"guinier_i0_error": 165.14,
"pddf_rg": 4.09,
"pddf_rg_error": 0.01,
"guinier_rg": 4.12,
"guinier_rg_error": 0.07,
"pddf_dmax": 11.35,
"pddf_dmax_error": null,
"porod_volume": 262.0,
"porod_volume_error": null,
"estimated_volume": 285.0,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 82,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDD33_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}
