{ "code": "SASDXV3", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/A", "project": { "title": "DNA induces non-canonical dimerization of the farnesoid X receptor.", "publication": { "title": "DNA induces non-canonical dimerization of the farnesoid X receptor.", "author_list": "Khan SH, Yennawar N, Okafor CD", "journal": "Nucleic Acids Res", "doi": "10.1093/nar/gkag087", "pmid": "41728955", "published_date": "2026 Feb 5" }, "status": "released", "submitted_date": "2025-04-16", "released_date": "2026-02-26" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDXV3.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDXV3.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXV3_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXV3_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDXV3_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXV3_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDXV3.sascif", "experiment": { "instrument": { "detector": { "type": "Hybrid Photon Counting (HPC) X-ray detector", "name": "Rigaku HyPix-3000", "resolution": 100.0 }, "name": "Pennsylvania State University", "city": "University Park, PA", "country": "USA", "beamline_name": "Rigaku BioSAXS-2000", "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": "inverted repeat DNA", "short_name": "IR1", "sequence": "CCGAGGTCAATGACCTCG\r\nCCGAGGTCATTGACCTCG", "organism": null, "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "DNA", "uniprot_sequence": "", "mw": 11.102, "total_mw": 11.102, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "" }, { "long_name": "Isoform 3 of Bile acid receptor", "short_name": "FXR", "sequence": "KKPRMGASAGRIKGDELCVVCGDRASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCVMDMYMRRKCQECRLRKCKEMGMLAECMYTGLLTEIQCKSKRLRKNVKQHADQTVNEDSEGRDLRQVTSTTKSCREKTELTPDQQTLLHFIMDSYNKQRMPQEITNKILKEEFSAEENFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPSGHSDLLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRVNDHKFT", "organism": "Homo sapiens", "uniprot_code": "Q96RI1", "uniprot_range_first": 110, "uniprot_range_last": 466, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MGSKMNLIEHSHLPTTDEFSFSENLFGVLTEQVAGPLGQNLEVEPYSQYSNVQFPQVQPQ\nISSSSYYSNLGFYPQQPEEWYSPGIYELRRMPAETLYQGETEVAEMPVTKKPRMGASAGR\nIKGDELCVVCGDRASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCVMDMYMRRKCQ\nECRLRKCKEMGMLAECMYTGLLTEIQCKSKRLRKNVKQHADQTVNEDSEGRDLRQVTSTT\nKSCREKTELTPDQQTLLHFIMDSYNKQRMPQEITNKILKEEFSAEENFLILTEMATNHVQ\nVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPSGHSDLLEERIRNSG\nISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQ\nKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRVNDHKFTPLLCEIWDVQ", "mw": 41.264, "total_mw": 82.528, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "" } ], "buffer": { "name": "50 mM HEPES, 150 mM NaCl, 5 % glycerol, 1 mM DTT, 20 µM CDCA", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.4, "deuteration": null }, "purity_method": null, "name": "Farnesoid X receptor homo-dimer bound to inverted repeat DNA", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "PSU", "address": "Pennsylvania, USA", "full_name": "Pennsylvania State University (PSU)", "webpage": "https://www.psu.edu/" } ], "contributor_name": "Neela", "contributor_surname": "Yennawar", "orcid": "" } ], "concentration_method": null, "concentration_unit": null, "date": "2024-05-09", "storage_temperature": 4.0, "cell_temperature": 4.0, "exposure_time": 600.0, "number_of_frames": 6, "wavelength": 0.154, "sample_detector_distance": 4.955, "concentration_min": null, "concentration_max": 0.6, "sample_volume": null, "flow_rate": null, "s_min": 0.034, "s_max": 6.106, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDXV3_fit1_model1_img.png", "software": "AlphaFold", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDXV3_fit1_model1.pdb", "model_mw": 93.05, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 1001 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDXV3_fit1_fixed_fit_img.png", "software": "FoXS", "chi_square_value": 1.939, "p_value": 0.0001, "fit_residual_plot": "SASDXV3_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDXV3_fit1.fit", "fit_log": null, "software_version": null, "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": null, "i0_calibration_standard": null, "description": "Chenodeoxycholic acid (CDCA): https://www.ebi.ac.uk/chembl/explore/compound/CHEMBL240597", "experiment_description": "SAXS data from solutions of farnesoid X receptor homo-dimer bound to inverted repeat DNA in 50 mM HEPES, 150 mM NaCl, 5 % glycerol, 1 mM DTT, 20 µM CDCA, pH 7.4 were collected on a Rigaku BioSAXS-2000 instrument (Pennsylvania State University, University Park, PA, USA) using a Rigaku HyPix-3000 detector at a sample-detector distance of 5.0 m and at a wavelength of λ = 0.154 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 0.60 mg/ml was measured at 4°C. Six successive 600 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": 94.7, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 6.051, "pddf_i0_error": null, "guinier_i0": 5.74754, "guinier_i0_error": null, "pddf_rg": 5.83, "pddf_rg_error": null, "guinier_rg": 5.05, "guinier_rg_error": 0.078, "pddf_dmax": 23.2, "pddf_dmax_error": null, "porod_volume": 120.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 9, "guinier_point_last": 28, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDXV3_datloglog_img.png", "symmetry": null, "last_modified": "2026-02-26T13:30:46.344061+01:00", "bragg_peak": [] }