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{
"code": "SASDBA7",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/A",
"project": {
"title": "Destabilization of the PCNA trimer mediated by its interaction with the NEIL1 DNA glycosylase.",
"publication": {
"title": "Destabilization of the PCNA trimer mediated by its interaction with the NEIL1 DNA glycosylase.",
"author_list": "Prakash A, Moharana K, Wallace SS, Doublié S",
"journal": "Nucleic Acids Res",
"doi": "10.1093/nar/gkw1282",
"pmid": "27994037",
"published_date": "2017 Mar 17"
},
"status": "released",
"submitted_date": "2016-11-04",
"released_date": "2017-01-03"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBA7.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBA7.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBA7_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBA7_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBA7_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBA7_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBA7.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": "Endonuclease 8-like 1",
"short_name": null,
"sequence": "MPEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRESVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQHRPSPELTLSQKIRTKLQNPDLLELCHSVPKEVVQLGGKGYGSESGEEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAPKGRKSRKKKSKATQLSPEDRVEDALPPSKAPSRTRRAKRDLPKRTATQRPEGTSLQQDPEAPTVPKKGRRKGRQAASGHCRPRKVKADIPSLEPEGTSASLEHHHHHH",
"organism": "Homo sapiens",
"uniprot_code": "Q96FI4",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MPEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLIL\nSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRF\nGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRA\nEILYRLKIPPFEKARSVLEALQQHRPSPELTLSQKIRTKLQNPDLLELCHSVPKEVVQLG\nGKGYGSESGEEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAPKGRKSRKKKS\nKATQLSPEDRVEDALPPSKAPSRTRRAKRDLPKRTATQRPEGTSLQQDPEAPTVPKKGRR\nKGRQAASGHCRPRKVKADIPSLEPEGTSAS",
"mw": 44.722,
"total_mw": 44.722,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "dsDNA",
"short_name": null,
"sequence": "GCGTCCAGTCTACC\r\nCGCAGGTCCAGATGG",
"organism": null,
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "DNA",
"uniprot_sequence": null,
"mw": 2.424,
"total_mw": 2.424,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Proliferating cell nuclear antigen",
"short_name": null,
"sequence": "MHHHHHHMFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFACICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDEEGS",
"organism": "Homo sapiens",
"uniprot_code": "P12004",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTY\nRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMD\nLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNI\nKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYK\nIADMGHLKYYLAPKIEDEEGS",
"mw": 29.669,
"total_mw": 29.669,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "25mM HEPES 100mM NaCl 1mM DTT",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Human NEI like DNA glycosylase 1 (NEIL1) bound to Proliferating Cell Nuclear Antigen (PCNA) and DNA",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Burlington, VT, USA",
"full_name": "University of Vermont",
"webpage": "https://www.uvm.edu/"
}
],
"contributor_name": "Kedar",
"contributor_surname": "Moharana",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2016-01-20",
"storage_temperature": 4.0,
"cell_temperature": 10.0,
"exposure_time": 0.2,
"number_of_frames": 24,
"wavelength": 0.1127,
"sample_detector_distance": 1.4,
"concentration_min": 0.6,
"concentration_max": 2.8,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.164,
"s_max": 5.285,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBA7_fit1_model1_img.png",
"software": "DAMMIN",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBA7_fit1_model1.pdb",
"model_mw": null,
"bead_radius": 4.2,
"log": null,
"symmetry": "",
"comment": "",
"user": 177
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBA7_fit1_fit_img.png",
"software": null,
"chi_square_value": 0.477,
"p_value": 0.000464,
"fit_residual_plot": "SASDBA7_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBA7_fit1.fir",
"fit_log": null,
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBA7_fit2_model1_img.png",
"software": "DAMMIN",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBA7_fit2_model1.pdb",
"model_mw": null,
"bead_radius": 4.2,
"log": null,
"symmetry": "",
"comment": "",
"user": 177
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBA7_fit2_fit_img.png",
"software": null,
"chi_square_value": 0.476,
"p_value": 0.000464,
"fit_residual_plot": "SASDBA7_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBA7_fit2.fir",
"fit_log": null,
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBA7_fit3_model1_img.png",
"software": "DAMMIN",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBA7_fit3_model1.pdb",
"model_mw": null,
"bead_radius": 4.2,
"log": null,
"symmetry": "",
"comment": "",
"user": 177
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBA7_fit3_fit_img.png",
"software": null,
"chi_square_value": 0.481,
"p_value": 0.000464,
"fit_residual_plot": "SASDBA7_fit3_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBA7_fit3.fir",
"fit_log": null,
"software_version": null,
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "ATSAS GNOM 5.0",
"i0_calibration_standard": null,
"description": "We have attempted to characterize this novel complex using SAXS. This complex shows prominent concentration dependency. Due to presence of DNA as part of this complex, \"280nm UV absorbance\"-based concentration estimations have been largely compromised, producing un-interpretable forward scattering upon concentration normalization. Thus we have relied upon the \"concentration-independent\" SAXS-MoW to estimate the MW of the scatterer at physiologically relevant micromolar concentrations. MW estimated using qmax=0.2431 (<=8/Rg) suggests this novel complex to be 86.7kDa, comparable to theoretical value of 85.5 kDa.",
"experiment_description": null,
"tags": [],
"intensity_unit": null,
"experimental_mw": 86.7,
"experimental_mw_error": null,
"guinier_i0_mw": 130.38,
"guinier_i0_mw_error": 1.29,
"porod_mw": 66.585,
"porod_mw_error": null,
"pddf_i0": 733.0,
"pddf_i0_error": 16.33,
"guinier_i0": 707.9,
"guinier_i0_error": 7.04,
"pddf_rg": 3.78,
"pddf_rg_error": 0.14,
"guinier_rg": 3.4,
"guinier_rg_error": 0.077,
"pddf_dmax": 16.4,
"pddf_dmax_error": 0.5,
"porod_volume": 113.2,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 39,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDBA7_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
