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{
"code": "SASDX87",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Molecular architecture of the human citrate synthase–malate dehydrogenase 2 metabolon",
"publication": {
"title": "Molecular architecture of the human citrate synthase–malate dehydrogenase 2 metabolon",
"author_list": "Kayll A, Rupakheti U, St John R, Rementeria G, Provost J, Berndsen C",
"journal": "Acta Crystallographica Section D Structural Biology",
"doi": "10.1107/S2059798326005802",
"pmid": null,
"published_date": "2026 Jun 21"
},
"status": "released",
"submitted_date": "2025-08-01",
"released_date": "2026-06-27"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDX87.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDX87.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX87_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX87_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDX87_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX87_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDX87.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus3 X 2M",
"resolution": 172.0
},
"name": "Advanced Light Source (ALS)",
"city": "Berkeley, CA",
"country": "USA",
"beamline_name": "12.3.1 (SIBYLS)",
"beam_geometry": "",
"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": "citrate synthase",
"short_name": "hCS",
"sequence": "MDHHHHHHENLYFQGASSTNLKDILADLIPKEQARIKTFRQQHGKTVVGQITVDMMYGGMRGMKGLVYETSVLDPDEGIRFRGFSIPECQKLLPKAKGGEEPLPEGLFWLLVTGHIPTEEQVSWLSKEWAKRAALPSHVVTMLDNFPTNL\r\nHPMSQLSAAVTALNSESNFARAYANGISRTKYWELIYEDSMDLIAKLPCVAAKIYRNLYREGSGIGAIDSNLDWSHNFTNMLGYTDHQFTELTRLYLTIHSDHEGGNVSAHTSHLVGSALSDPYLSFAAAMNGLAGPLHGLANQEVLVWLTQLQKEVGKDVSDEKLRDYIWNTLNSGRVVPGYGHAVLRKTDPRYTCQREFALKHLPNDPMFKLVAQLYKIVPNVLLEQGKAKNPWPNVDAHSGVLLQYYGMTEMNYYTVLFGVSRALGVLAQLIWSRALGFPLERPKSMSTEGLMKFVDSKSG",
"organism": "Homo sapiens",
"uniprot_code": "O75390",
"uniprot_range_first": 28,
"uniprot_range_last": 466,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MALLTAAARLLGTKNASCLVLAARHASASSTNLKDILADLIPKEQARIKTFRQQHGKTVV\nGQITVDMMYGGMRGMKGLVYETSVLDPDEGIRFRGFSIPECQKLLPKAKGGEEPLPEGLF\nWLLVTGHIPTEEQVSWLSKEWAKRAALPSHVVTMLDNFPTNLHPMSQLSAAVTALNSESN\nFARAYAQGISRTKYWELIYEDSMDLIAKLPCVAAKIYRNLYREGSGIGAIDSNLDWSHNF\nTNMLGYTDHQFTELTRLYLTIHSDHEGGNVSAHTSHLVGSALSDPYLSFAAAMNGLAGPL\nHGLANQEVLVWLTQLQKEVGKDVSDEKLRDYIWNTLNSGRVVPGYGHAVLRKTDPRYTCQ\nREFALKHLPNDPMFKLVAQLYKIVPNVLLEQGKAKNPWPNVDAHSGVLLQYYGMTEMNYY\nTVLFGVSRALGVLAQLIWSRALGFPLERPKSMSTEGLMKFVDSKSG",
"mw": 50.913,
"total_mw": 101.8,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "human citrate synthase in a pET28a vector"
}
],
"buffer": {
"name": "50 mM Tris, 100 mM NaCl, 0.1 mM EDTA",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "human Citrate Synthase",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Harrisonburg, Virginia, USA",
"full_name": "James Madison University",
"webpage": "https://www.jmu.edu/"
}
],
"contributor_name": "Christopher",
"contributor_surname": "Berndsen",
"orcid": "https://orcid.org/0000-0002-4285-4341"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2024-06-25",
"storage_temperature": null,
"cell_temperature": null,
"exposure_time": null,
"number_of_frames": null,
"wavelength": null,
"sample_detector_distance": null,
"concentration_min": null,
"concentration_max": null,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.109,
"s_max": 4.702,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDX87_fit1_model1_img.png",
"software": "Other",
"pdb_link": [],
"model_title": null,
"type_of_model": "other",
"software_version": "NRGTEN",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDX87_fit1_model1.fit",
"model_mw": null,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 394
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDX87_fit1_fixed_fit_img.png",
"software": "FoXS",
"chi_square_value": 0.683201,
"p_value": 0.1807,
"fit_residual_plot": "SASDX87_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDX87_fit1.fit",
"fit_log": null,
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "For hCS, we used SEC-SAXS and HT-SAXS to describe the structure, while we used SEC-SAXS for the hMDH2-hCS crosslinked sample. hCS was diluted to a concentration ranging from 0.07 mg mL-1 to 2.0 mg mL-1 in size-exclusion buffer (50 mM Tris-Cl, 100 mM NaCl, and 0.1 mM EDTA, pH 7.5) and then placed into a 96-well plate. The samples were frozen at -80 ºC before shipment. Data were collected at SIBYLS beamline 12.3.1 at the Advanced Light Source, Lawrence Berkeley National Laboratory (Classen et al., 2013; Rosenberg et al., 2022). Before sample collection, the sample plate was spun at 3700 rev min-1 for 10 minutes. Samples were held at 10 ºC during collection. The exposure was 15 seconds, with frames collected every 0.3 seconds for 40 frames per sample. The incident light wavelength was 1.03 Å at a sample-to-detector distance of 2.1 m. This setup results in scattering vectors, q, ranging from 0.013 to 0.5 Å−1, where the scattering vector is defined as q = 4πsinθ/λ, and 2θ is the measured scattering angle. \r\nFor SEC-SAXS, samples were separated on a Shodex KW-803 column at a flow rate of 0.5 mL/min at 10 °C, and eluate was measured in-line with UV/vis absorbance at 280 nm, Multi-Angle X-ray Scattering (MALS), and SAXS. The column buffer was 50 mM sodium phosphate, pH 7, 100 mM NaCl, 2 mM DTT, and 2% glycerol. The incident light wavelength was 1.03 Å at a sample-to-detector distance of 2.1 m. \r\nTo process SEC-SAXS data, Chromixs was used to subtract buffer from the peaks and produce the initial data file (Panjkovich & Svergun, 2018; Manalastas-Cantos et al., 2021). We then used RAW to analyze the data and generate statistics for the processed SEC-SAXS and HT-SAXS data and FOXS to fit structural models to SAXS data (Schneidman-Duhovny et al., 2013; Hopkins, 2024).",
"experiment_description": null,
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 86.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 93.5,
"porod_mw_error": null,
"pddf_i0": 4.116,
"pddf_i0_error": 0.12,
"guinier_i0": 4.23976,
"guinier_i0_error": null,
"pddf_rg": 3.03,
"pddf_rg_error": 0.05,
"guinier_rg": 3.115,
"guinier_rg_error": 1.548,
"pddf_dmax": 9.6,
"pddf_dmax_error": null,
"porod_volume": 113.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 8,
"guinier_point_last": 61,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDX87_datloglog_img.png",
"symmetry": null,
"last_modified": "2026-06-27T16:58:21.494947+02:00",
"bragg_peak": []
}
