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{
"code": "SASDDB3",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/A",
"project": {
"title": "Architectural Features of Human Mitochondrial Cysteine Desulfurase Complexes from Crosslinking Mass Spectrometry and Small-Angle X-Ray Scattering.",
"publication": {
"title": "Architectural Features of Human Mitochondrial Cysteine Desulfurase Complexes from Crosslinking Mass Spectrometry and Small-Angle X-Ray Scattering.",
"author_list": "Cai K, Frederick RO, Dashti H, Markley JL",
"journal": "Structure",
"doi": "10.1016/j.str.2018.05.017",
"pmid": "29983374",
"published_date": "2018 Aug 7"
},
"status": "released",
"submitted_date": "2018-01-26",
"released_date": "2018-05-16"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDB3.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDB3.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDB3_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDB3_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDB3_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDB3_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDB3.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "MikroGap gas detector",
"name": "VÅNTEC-2000",
"resolution": 200.0
},
"name": "NMRFAM",
"city": "Madison, WI",
"country": "USA",
"beamline_name": "Bruker Nanostar",
"beam_geometry": null,
"type_of_source": "X-ray in house",
"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": "Cysteine desulfurase, mitochondrial",
"short_name": "NFS1",
"sequence": ">sp|Q9Y697|NFS1_HUMAN Cysteine desulfurase, mitochondrial OS=Homo sapiens GN=NFS1 PE=1 SV=3\r\nGPVLRPLYMDVQATTPLDPRVLDAMLPYLINYYGNPHSRTHAYGWESEAAMERARQQVASLIGADPRE\r\nIIFTSGATESNNIAIKGVARFYRSRKKHLITTQTEHKCVLDSCRSLEAEGFQVTYLPVQK\r\nSGIIDLKELEAAIQPDTSLVSVMTVNNEIGVKQPIAEIGRICSSRKVYFHTDAAQAVGKI\r\nPLDVNDMKIDLMSISGHKIYGPKGVGAIYIRRRPRVRVEALQSGGGQERGMRSGTVPTPL\r\nVVGLGAACEVAQQEMEYDHKRISKLSERLIQNIMKSLPDVVMNGDPKHHYPGCINLSFAY\r\nVEGESLLMALKDVALSSGSACTSASLEPSYVLRAIGTDEDLAHSSIRFGIGRFTTEEEVD\r\nYTVEKCIQHVKRLREMSPLWEMVQDGIDLKSIKWTQH",
"organism": "Homo sapiens",
"uniprot_code": "Q9Y697",
"uniprot_range_first": 53,
"uniprot_range_last": 457,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MLLRAAWRRAAVAVTAAPGPKPAAPTRGLRLRVGDRAPQSAVPADTAAAPEVGPVLRPLY\nMDVQATTPLDPRVLDAMLPYLINYYGNPHSRTHAYGWESEAAMERARQQVASLIGADPRE\nIIFTSGATESNNIAIKGVARFYRSRKKHLITTQTEHKCVLDSCRSLEAEGFQVTYLPVQK\nSGIIDLKELEAAIQPDTSLVSVMTVNNEIGVKQPIAEIGRICSSRKVYFHTDAAQAVGKI\nPLDVNDMKIDLMSISGHKIYGPKGVGAIYIRRRPRVRVEALQSGGGQERGMRSGTVPTPL\nVVGLGAACEVAQQEMEYDHKRISKLSERLIQNIMKSLPDVVMNGDPKHHYPGCINLSFAY\nVEGESLLMALKDVALSSGSACTSASLEPSYVLRAIGTDEDLAHSSIRFGIGRFTTEEEVD\nYTVEKCIQHVKRLREMSPLWEMVQDGIDLKSIKWTQH",
"mw": 44.913,
"total_mw": 89.826,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "LYR motif-containing protein 4",
"short_name": "ISD11",
"sequence": ">sp|Q9HD34|LYRM4_HUMAN LYR motif-containing protein 4 OS=Homo sapiens GN=LYRM4 PE=1 SV=1\r\nMAASSRAQVLSLYRAMLRESKRFSAYNYRTYAVRRIRDAFRENKNVKDPVEIQTLVNKAK\r\nRDLGVIRRQVHIGQLYSTDKLIIENRDMPRTHHHHHH",
"organism": "Homo sapiens",
"uniprot_code": "Q9HD34",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MAASSRAQVLSLYRAMLRESKRFSAYNYRTYAVRRIRDAFRENKNVKDPVEIQTLVNKAK\nRDLGVIRRQVHIGQLYSTDKLIIENRDMPRT",
"mw": 11.581,
"total_mw": 23.162,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Acyl carrier protein",
"short_name": null,
"sequence": "P>sp|P0A6A8|ACP_ECOLI Acyl carrier protein OS=Escherichia coli (strain K12) GN=acpP PE=1 SV=2\r\nMSTIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTVELVMALEEEFDTEIPDEEA\r\nEKITTVQAAIDYINGHQA",
"organism": "Escherichia coli",
"uniprot_code": "P0A6A8",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MSTIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTVELVMALEEEFDTEIPDEEA\nEKITTVQAAIDYINGHQA",
"mw": 11.5,
"total_mw": 22.0,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM HEPES, 150 mM NaCl, 5 mM TCEP",
"concentration_unit": null,
"comment": "HNT Buffer",
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Human mitochondrial cysteine desulfurase (NFS1, ISD11 and Acp heterodimer complex)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Madison, WI, USA",
"full_name": "University of Wisconsin-Madison",
"webpage": "https://www.wisc.edu/"
}
],
"contributor_name": "Kai",
"contributor_surname": "Cai",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-05-22",
"storage_temperature": 4.0,
"cell_temperature": 25.0,
"exposure_time": 3600.0,
"number_of_frames": 4,
"wavelength": 0.15418,
"sample_detector_distance": 1.0,
"concentration_min": 2.0,
"concentration_max": 10.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.0,
"s_max": 2.56,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDB3_fit1_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "5wgb",
"ext_code": "5WGB",
"ext_type": "pdb",
"difference_with_model": "identical"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDB3_fit1_model1.pdb",
"model_mw": 92.29,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 279
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDB3_fit1_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.149112,
"p_value": 0.253126,
"fit_residual_plot": null,
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDB3_fit1.fit",
"fit_log": null,
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDB3_fit2_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "5usr",
"ext_code": "5USR",
"ext_type": "pdb",
"difference_with_model": "identical"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDB3_fit2_model1.pdb",
"model_mw": 111.5,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 279
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDB3_fit2_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 2.617924,
"p_value": 0.0,
"fit_residual_plot": null,
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDB3_fit2.fit",
"fit_log": null,
"software_version": null,
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "4.5a",
"i0_calibration_standard": null,
"description": "Solution SAXS study the human mitochondrial cysteine desulfurase, which consists of three components: NFS1, ISD11 and Acp and forms a homodimer.",
"experiment_description": "SAXS data from solutions of human mitochondrial cysteine desulfurase (NFS1, ISD11 and Acp heterodimer complex) in 20 mM HEPES, 150 mM NaCl, 5 mM TCEP, pH 7.5 were collected on a Bruker Nanostar instrument (Madison, WI, USA) using a MikroGap Vantec-2000 detector at a sample-detector distance of 1 m and at a wavelength of λ = 0.15418 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 2 and 10 mg/ml were measured at 25°C. Four successive 3600 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": 125.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 906.7,
"pddf_i0_error": null,
"guinier_i0": 931.8,
"guinier_i0_error": 8.7,
"pddf_rg": 3.65,
"pddf_rg_error": 0.05,
"guinier_rg": 3.7,
"guinier_rg_error": 0.46,
"pddf_dmax": 11.83,
"pddf_dmax_error": 0.5,
"porod_volume": 203.5,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 12,
"guinier_point_last": 26,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDDB3_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
