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": "SASDWM2",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Structural basis for the recognition and ubiquitylation of type-2 N-degron substrate by PRT1 plant N-recognin",
"publication": {
"title": "Structural basis for the recognition and ubiquitylation of type-2 N-degron substrate by PRT1 plant N-recognin",
"author_list": "Yang W, Kim S, Kim M, Shin H, Lee J, Sandmann A, Park O, Dissmeyer N, Song H",
"journal": "Nature Communications",
"doi": "10.1038/s41467-025-63282-9",
"pmid": null,
"published_date": "2025 Aug 21"
},
"status": "released",
"submitted_date": "2024-11-26",
"released_date": "2025-08-22"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDWM2.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDWM2.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWM2_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWM2_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDWM2_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWM2_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDWM2.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus3 2M",
"resolution": 0.172
},
"name": "Photon Factory (PF), High Energy Accelerator Research Organization (KEK)",
"city": "Tsukuba",
"country": "Japan",
"beamline_name": "BL-10C",
"beam_geometry": null,
"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": "E3 ubiquitin-protein ligase PRT1",
"short_name": "PRT1",
"sequence": "MAETMKDITMKNDESQEEEIPDQFLCCVCLELLYKPIVLSCGHLSCFWCVHKSMNGFRESHCPICRDPYVHFPSVCQKLYFLLKKMYPLAHKKREEQVLKEEQERECFSPQIDLVLDLSVCSGDSLNVSDKQKVEECSNAANLLSSSSSRGDIPCIPKNQEPTDAKALNVHENELLKDNKVSKQISKDDLLCSACKELLVRPVVLNCGHVYCEGCVVDMAEESEKIKCQECNVCDPRGFPKVCLILEQLLEENFPEEYNSRSSKVQKTLAHNSKGNIQSYLKEGPSLSNDNNNDDPWLANPGSNVHFGAGCDSCGVYPIIGDRYRCKDCKEEIGYDLCKDCYETPSKVPGRFNQQHTPDHRLELARSPQVLINFNSIGILLGPVISNEGMDTDEGEEGPPGSSNESSSTE",
"organism": "Arabidopsis thaliana",
"uniprot_code": "Q8LBL5",
"uniprot_range_first": 1,
"uniprot_range_last": 410,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MAETMKDITMKNDESQEEEIPDQFLCCVCLELLYKPIVLSCGHLSCFWCVHKSMNGFRES\nHCPICRDPYVHFPSVCQKLYFLLKKMYPLAHKKREEQVLKEEQERECFSPQIDLVLDLSV\nCSGDSLNVSDKQKVEECSNAANLLSSSSSRGDIPCIPKNQEPTDAKALNVHENELLKDNK\nVSKQISKDDLLCSACKELLVRPVVLNCGHVYCEGCVVDMAEESEKIKCQECNVCDPRGFP\nKVCLILEQLLEENFPEEYNSRSSKVQKTLAHNSKGNIQSYLKEGPSLSNDNNNDDPWLAN\nPGSNVHFGAGCDSCGVYPIIGDRYRCKDCKEEIGYDLCKDCYETPSKVPGRFNQQHTPDH\nRLELARSPQVLINFNSIGILLGPVISNEGMDTDEGEEGPPGSSNESSSTE",
"mw": 45.936,
"total_mw": 45.936,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": ""
}
],
"buffer": {
"name": "50 mM Tris-HCl, 150 mM NaCl, 1 mM TCEP, 2% w/v glycerol",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Wild-type E3 ubiquitin-protein ligase PRT1 (Proteolysis1)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "South Korea",
"full_name": "Korea University",
"webpage": "https://www.korea.edu/"
}
],
"contributor_name": "Woo Seok",
"contributor_surname": "Yang",
"orcid": "https://orcid.org/0000-0002-0022-0295"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2018-05-22",
"storage_temperature": 25.0,
"cell_temperature": 25.0,
"exposure_time": 20.0,
"number_of_frames": 328,
"wavelength": 0.15,
"sample_detector_distance": 3.0,
"concentration_min": null,
"concentration_max": 10.0,
"sample_volume": 250.0,
"flow_rate": 0.05,
"s_min": 0.033,
"s_max": 2.809,
"total_exposure_time": null,
"seccolumn": 1
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDWM2_fit1_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDWM2_fit1_model1.pdb",
"model_mw": 40.042,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/final_2_7Z2QyHq.log",
"symmetry": null,
"comment": null,
"user": 1153
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWM2_fit1_fixed_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 1.152,
"p_value": 0.4594,
"fit_residual_plot": "SASDWM2_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDWM2_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/final_2.log",
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDWM2_fit2_model1_img.png",
"software": "AlphaFold Protein Structure Database",
"pdb_link": [
{
"pdb_code": "none",
"ext_code": "Q8LBL5",
"ext_type": "alphafold",
"difference_with_model": "identical"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDWM2_fit2_model1.pdb",
"model_mw": 46.3,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/AF-Q8LBL5-F1-model_v4_5.log",
"symmetry": null,
"comment": null,
"user": 1153
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWM2_fit2_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.734,
"p_value": 0.0,
"fit_residual_plot": "SASDWM2_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDWM2_fit2.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": null,
"experiment_description": "Synchrotron SAXS data from solutions of PRT1 in 50 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM TCEP, and 2% (w/v) glycerol were collected on the BL-10C beam line at the Photon Factory (PF), High Energy Accelerator Research Organization (KEK; Tsukuba, Japan) using a Pilatus3 2M detector at a sample-detector distance of 3.0 m and at a wavelength of λ = 0.15 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 250.00 μl sample at 10 mg/ml was injected at different flow rates in the protein peak (20 sec/image with flow at 0.05 ml/min) and the base line (20 sec/image with flow at 0.5 ml/min) using a GE Superdex 200 Increase 10/300 column at 25°C. 332 successive 20-second frames were collected.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 46.6,
"experimental_mw_error": null,
"guinier_i0_mw": 44.3,
"guinier_i0_mw_error": 3.9,
"porod_mw": 38.0,
"porod_mw_error": null,
"pddf_i0": 0.1663,
"pddf_i0_error": 0.002,
"guinier_i0": 0.164412,
"guinier_i0_error": null,
"pddf_rg": 3.632,
"pddf_rg_error": 0.6,
"guinier_rg": 3.429,
"guinier_rg_error": 0.58,
"pddf_dmax": 12.68,
"pddf_dmax_error": null,
"porod_volume": 60.7,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 27,
"guinier_point_last": 145,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDWM2_datloglog_img.png",
"symmetry": null,
"last_modified": "2025-08-22T03:11:39.462006+02:00",
"bragg_peak": []
}
