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.
View the complete summary.json source
{
"code": "SASDBR3",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "RNF8 E3 Ubiquitin Ligase Stimulates Ubc13 E2 Conjugating Activity That Is Essential for DNA Double Strand Break Signaling and BRCA1 Tumor Suppressor Recruitment.",
"publication": {
"title": "RNF8 E3 Ubiquitin Ligase Stimulates Ubc13 E2 Conjugating Activity That Is Essential for DNA Double Strand Break Signaling and BRCA1 Tumor Suppressor Recruitment.",
"author_list": "Hodge CD, Ismail IH, Edwards RA, Hura GL, Xiao AT, Tainer JA, Hendzel MJ, Glover JN",
"journal": "J Biol Chem",
"doi": "10.1074/jbc.M116.715698",
"pmid": "26903517",
"published_date": "2016 Apr 29"
},
"status": "released",
"submitted_date": "2016-02-11",
"released_date": "2016-08-31"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBR3.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBR3.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBR3_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBR3_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBR3_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBR3_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBR3.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": "E3 ubiquitin-protein ligase RNF8",
"short_name": "RNF8",
"sequence": "GPLGSPEFQEHWALMEELNRSKKDFEAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCINKMVNNLSSEVKERRIVLIRERKAKRLF",
"organism": "Homo sapiens",
"uniprot_code": "O76064",
"uniprot_range_first": 345,
"uniprot_range_last": 485,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MGEPGFFVTGDRAGGRSWCLRRVGMSAGWLLLEDGCEVTVGRGFGVTYQLVSKICPLMIS\nRNHCVLKQNPEGQWTIMDNKSLNGVWLNRARLEPLRVYSIHQGDYIQLGVPLENKENAEY\nEYEVTEEDWETIYPCLSPKNDQMIEKNKELRTKRKFSLDELAGPGAEGPSNLKSKINKVS\nCESGQPVKSQGKGEVASTPSDNLDPKLTALEPSKTTGAPIYPGFPKVTEVHHEQKASNSS\nASQRSLQMFKVTMSRILRLKIQMQEKHEAVMNVKKQTQKGNSKKVVQMEQELQDLQSQLC\nAEQAQQQARVEQLEKTFQEEEQHLQGLEIAQGEKDLKQQLAQALQEHWALMEELNRSKKD\nFEAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYFIEAVTLNCAH\nSFCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCINKMVNNLSSEVKERRIVLIRERK\nAKRLF",
"mw": 17.618,
"total_mw": 35.237,
"number_molecules": 2,
"complex_state": null,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A)",
"short_name": "Ubc13 - C87K, K92A",
"sequence": "GPLGSPEFMAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRIKLDILADKWSPALQIRTVLLSIQALLSAPNPDDP\r\nLANDVAEQWKTNEAQAIETARAWTRLYAMNNI\r\n",
"organism": "Homo sapiens",
"uniprot_code": "P61088",
"uniprot_range_first": 1,
"uniprot_range_last": 152,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPE\nEYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDP\nLANDVAEQWKTNEAQAIETARAWTRLYAMNNI",
"mw": 17.89,
"total_mw": 35.781,
"number_molecules": 2,
"complex_state": null,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Polyubiquitin-C",
"short_name": "UBC",
"sequence": "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN\r\nIQKESTLHLVLRLRGG",
"organism": "Homo sapiens",
"uniprot_code": "P0CG48",
"uniprot_range_first": 1,
"uniprot_range_last": 76,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN\nIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI\nFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKA\nKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKT\nITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR\nLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL\nSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ\nQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIE\nNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTL\nTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLH\nLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLED\nGRTLSDYNIQKESTLHLVLRLRGGV",
"mw": 8.565,
"total_mw": 17.129,
"number_molecules": 2,
"complex_state": null,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM HEPES 200 mM NaCl 0.01 mM ZnSO4 1 mM DTT",
"concentration_unit": "mM",
"comment": null,
"additive": "200 mM NaCl, 0.01 mM, ZnSO4, and 1 mM DTT",
"concentration": 20.0,
"pka": null,
"ph": 6.8,
"deuteration": null
},
"purity_method": null,
"name": "Wild type RNF8 complexed with Ubc13 (C87K, K92A mutant): conjugated to Ubiquitin",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Edmonton, AB T6G 2R3, Canada",
"full_name": "University of Alberta",
"webpage": ""
}
],
"contributor_name": "Ross",
"contributor_surname": "Edwards",
"orcid": null
},
{
"affiliation": [
{
"short_name": null,
"address": "Edmonton, AB T6G 2R3, Canada",
"full_name": "University of Alberta",
"webpage": ""
}
],
"contributor_name": "Mark",
"contributor_surname": "Glover",
"orcid": null
},
{
"affiliation": [
{
"short_name": null,
"address": "Edmonton, AB T6G 2R3, Canada",
"full_name": "University of Alberta",
"webpage": ""
}
],
"contributor_name": "Curtis",
"contributor_surname": "Hodge",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2015-09-08",
"storage_temperature": null,
"cell_temperature": null,
"exposure_time": null,
"number_of_frames": null,
"wavelength": 0.103,
"sample_detector_distance": null,
"concentration_min": null,
"concentration_max": null,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.139,
"s_max": 4.096,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBR3_fit1_model1_img.png",
"software": "MES-FoXS",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBR3_fit1_model1.pdb",
"model_mw": 225.2,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 110
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBR3_fit1_model2_img.png",
"software": "MES-FoXS",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBR3_fit1_model2.pdb",
"model_mw": 225.2,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 110
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBR3_fit1_model3_img.png",
"software": "MES-FoXS",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBR3_fit1_model3.pdb",
"model_mw": 225.2,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 110
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBR3_fit1_model4_img.png",
"software": "MES-FoXS",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBR3_fit1_model4.pdb",
"model_mw": 225.2,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 110
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBR3_fit1_model5_img.png",
"software": "MES-FoXS",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBR3_fit1_model5.pdb",
"model_mw": 225.2,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 110
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBR3_fit1_fit_img.png",
"software": null,
"chi_square_value": 1.3755,
"p_value": 0.0,
"fit_residual_plot": "SASDBR3_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBR3_fit1.fit",
"fit_log": null,
"software_version": null,
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": null,
"experiment_description": "X-ray synchrotron radiation scattering data from solutions of the 2:2:2 complex formed between E3 ubiquitin-protein ligase RNF8, Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A) and Polyubiquitin-C in 20 mM HEPES 200 mM NaCl, 0.01 mM, ZnSO4, and 1 mM DTT were collected on the BL12.3.1 SIBYLS camera on the ALS storage ring (Berkeley, CA, USA) using a Pilatus 2M detector (s = 4π sin θ/λ, where 2θ is the scattering angle). The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the curves were scaled for protein concentration. The models shown in this entry were generated in BILBOMD from an initial pool of 4740 structures. The theoretical scattering profiles for those models were calculated using FoXS, and FoXS was also used to run a minimal ensemble search (MES). The percent contribution to the MES is written in the header of each of the PDB file, expressed as a volume fraction. For the models displayed in this entry, the volume-fractions are (from top to bottom): 0.44, 0.41, 0.07, 0.06 and 0.01. The fit of the MES was calculated using FoXS.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 66.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 665.1,
"pddf_i0_error": null,
"guinier_i0": 662.4,
"guinier_i0_error": null,
"pddf_rg": 4.63,
"pddf_rg_error": null,
"guinier_rg": 4.45,
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"pddf_dmax": 18.85,
"pddf_dmax_error": null,
"porod_volume": 119.05,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 2,
"guinier_point_last": 14,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDBR3_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
