{ "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": [] }