The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
Every source field is expanded here, including empty values, list members and fields already shown above.
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{
"code": "SASDAV6",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "Structural bases for the interaction of frataxin with the central components of iron-sulphur cluster assembly.",
"publication": {
"title": "Structural bases for the interaction of frataxin with the central components of iron-sulphur cluster assembly.",
"author_list": "Prischi F, Konarev PV, Iannuzzi C, Pastore C, Adinolfi S, Martin SR, Svergun DI, Pastore A",
"journal": "Nat Commun",
"doi": "10.1038/ncomms1097",
"pmid": "20981023",
"published_date": "2010 Oct 19"
},
"status": "released",
"submitted_date": null,
"released_date": "2015-07-07"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDAV6.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDAV6.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAV6_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAV6_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDAV6_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAV6_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDAV6.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",
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"xray_energy": null,
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},
"sample": {
"molecule": [
{
"long_name": "Cysteine desulfurase IscS",
"short_name": null,
"sequence": "KLPIYLDYSATTPVDPRVAEKMMQFMTMDGTFGNPASRSHRFGWQAEEAVDIARNQIADLVGADPREIVFTSGATESDNL\r\nAIKGAANFYQKKGKHIITSKTEHKAVLDTCRQLEREGFEVTYLAPQRNGIIDLKELEAAMRDDTILVSIMHVNNEIGVVQ\r\nDIAAIGEMCRARGIIYHVDATQSVGKLPIDLSQLKVDLMSFSGHKIYGPKGIGALYVRRKPRVRIEAQMHGGGHERGMRS\r\nGTLPVHQIVGMGEAYRIAKEEMATEMERLRGLRNRLWNGIKDIEEVYLNGDLEHGAPNILNVSFNYVEGESLIMALKDLA\r\nVSSGSACTSASLEPSYVLRALGLNDELAHSSIRFSLGRFTTEEEIDYTIELVRKSIGRLRDLSPLWEMYKQ",
"organism": "Escherichia coli",
"uniprot_code": "P0A6B7",
"uniprot_range_first": null,
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"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MKLPIYLDYSATTPVDPRVAEKMMQFMTMDGTFGNPASRSHRFGWQAEEAVDIARNQIAD\nLVGADPREIVFTSGATESDNLAIKGAANFYQKKGKHIITSKTEHKAVLDTCRQLEREGFE\nVTYLAPQRNGIIDLKELEAAMRDDTILVSIMHVNNEIGVVQDIAAIGEMCRARGIIYHVD\nATQSVGKLPIDLSQLKVDLMSFSGHKIYGPKGIGALYVRRKPRVRIEAQMHGGGHERGMR\nSGTLPVHQIVGMGEAYRIAKEEMATEMERLRGLRNRLWNGIKDIEEVYLNGDLEHGAPNI\nLNVSFNYVEGESLIMALKDLAVSSGSACTSASLEPSYVLRALGLNDELAHSSIRFSLGRF\nTTEEEIDYTIELVRKSIGRLRDLSPLWEMYKQGVDLNSIEWAHH",
"mw": 43.597,
"total_mw": 87.194,
"number_molecules": 2,
"complex_state": null,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Tris-HCl 150 mM NaCl 10 mM β-mercaptoethanol",
"concentration_unit": "mM",
"comment": null,
"additive": "150 mM NaCl and 10 mM β-mercaptoethanol",
"concentration": 20.0,
"pka": null,
"ph": 8.0,
"deuteration": null
},
"purity_method": null,
"name": "Cysteine desulfurase IscS dimer",
"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": "Petr",
"contributor_surname": "Konarev",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2009-11-05",
"storage_temperature": 15.0,
"cell_temperature": 15.0,
"exposure_time": 30.0,
"number_of_frames": 4,
"wavelength": 0.15,
"sample_detector_distance": 2.7,
"concentration_min": null,
"concentration_max": 2.5,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.077,
"s_max": 6.237,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDAV6_fit1_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "1p3w",
"ext_code": "1P3W",
"ext_type": "pdb",
"difference_with_model": null
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDAV6_fit1_model1.pdb",
"model_mw": 87.0,
"bead_radius": 1.9,
"log": null,
"symmetry": "P2",
"comment": "",
"user": 88
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAV6_fit1_fit_img.png",
"software": null,
"chi_square_value": 1.565001,
"p_value": 0.0,
"fit_residual_plot": "fit4columns179_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDAV6_fit1.fit",
"fit_log": null,
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDAV6_fit2_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDAV6_fit2_model1.pdb",
"model_mw": null,
"bead_radius": 3.9,
"log": null,
"symmetry": "",
"comment": "",
"user": 88
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAV6_fit2_fit_img.png",
"software": null,
"chi_square_value": 1.192464,
"p_value": 0.02187,
"fit_residual_plot": "SASDAV6_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDAV6_fit2.fir",
"fit_log": null,
"software_version": null,
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": "Reduced levels of frataxin, an essential protein of as yet unknown function, are responsible for causing the neurodegenerative pathology Friedreich’s ataxia. Independent reports have linked frataxin to iron–sulphur cluster assembly through interactions with the two central components of this machinery: desulphurase Nfs1/IscS and the scaffold protein Isu/IscU. In this study, we use a combination of biophysical methods to define the structural bases of the\r\ninteraction of CyaY (the bacterial orthologue of frataxin) with the IscS/IscU complex. We show that CyaY binds IscS as a monomer in a pocket between the active site and the IscS dimer interface. Recognition does not require iron and occurs through electrostatic interactions of complementary charged residues. Mutations at the complex interface affect the rates of enzymatic cluster formation. CyaY binding strengthens the affinity of the IscS/IscU complex. Our data suggest a new paradigm for understanding the role of frataxin as a regulator of IscS functions.",
"experiment_description": null,
"tags": [
"X33"
],
"intensity_unit": null,
"experimental_mw": 92.0,
"experimental_mw_error": null,
"guinier_i0_mw": 92.0,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 68.0,
"pddf_i0_error": null,
"guinier_i0": 68.0,
"guinier_i0_error": 0.14,
"pddf_rg": 3.19,
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"guinier_rg": 3.2,
"guinier_rg_error": 0.009,
"pddf_dmax": 10.9,
"pddf_dmax_error": null,
"porod_volume": null,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 54,
"guinier_point_last": null,
"pddf_point_first": 54,
"pddf_point_last": 1134,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDAV6_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-05-25T11:21:52.654103+02:00",
"bragg_peak": []
}
