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{
"code": "SASDVQ7",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/A",
"project": {
"title": "The strand exchange domain of tumor suppressor PALB2 is intrinsically disordered and promotes oligomerization-dependent DNA compaction.",
"publication": {
"title": "The strand exchange domain of tumor suppressor PALB2 is intrinsically disordered and promotes oligomerization-dependent DNA compaction.",
"author_list": "Kyriukha Y, Watkins MB, Redington JM, Chintalapati N, Ganti A, Dastvan R, Uversky VN, Hopkins JB, Pozzi N, Korolev S",
"journal": "iScience",
"doi": "10.1016/j.isci.2024.111259",
"pmid": "39584160",
"published_date": "2024 Dec 20"
},
"status": "released",
"submitted_date": "2024-10-05",
"released_date": "2024-12-23"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDVQ7.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVQ7.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVQ7_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVQ7_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVQ7_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVQ7_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVQ7.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Eiger 4M",
"resolution": 75.0
},
"name": "Cornell High Energy Synchrotron Source (CHESS)",
"city": "Ithaca, NY",
"country": "USA",
"beamline_name": "ID7A1 BioSAXS / HP-Bio Beamline",
"beam_geometry": null,
"type_of_source": "X-ray synchrotron",
"point_source": true,
"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": "Partner and localizer of BRCA2 (L24A)",
"short_name": "PALB2",
"sequence": "SMDEPPGKPLSCEEKEKLKEKLAFAKREYSKTLARLQRAQRAEKIKHSIKKTVEEQDCLSQQDLSPQLKHSEPKNKICVYDKLHIKTHLDEETGEKTSITLDVGPESFNPGDGPGGLPIQRTDDTQEHFPHRVSDPSGEQKQKLPSRRKKQQKRTFISQERDCVFGTDSLRLSGKRLKEQEEISSKNPARSPVTEWENLYFQS",
"organism": "Homo sapiens",
"uniprot_code": "Q86YC2",
"uniprot_range_first": 1,
"uniprot_range_last": 194,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MDEPPGKPLSCEEKEKLKEKLAFLKREYSKTLARLQRAQRAEKIKHSIKKTVEEQDCLSQ\nQDLSPQLKHSEPKNKICVYDKLHIKTHLDEETGEKTSITLDVGPESFNPGDGPGGLPIQR\nTDDTQEHFPHRVSDPSGEQKQKLPSRRKKQQKRTFISQERDCVFGTDSLRLSGKRLKEQE\nEISSKNPARSPVTEIRTHLLSLKSELPDSPEPVTEINEDSVLIPPTAQPEKGVDTFLRRP\nNFTRATTVPLQTLSDSGSSQHLEHIPPKGSSELTTHDLKNIRFTSPVSLEAQGKKMTVST\nDNLLVNKAISKSGQLPTSSNLEANISCSLNELTYNNLPANENQNLKEQNQTEKSLKSPSD\nTLDGRNENLQESEILSQPKSLSLEATSPLSAEKHSCTVPEGLLFPAEYYVRTTRSMSNCQ\nRKVAVEAVIQSHLDVKKKGFKNKNKDASKNLNLSNEETDQSEIRMSGTCTGQPSSRTSQK\nLLSLTKVSSPAGPTEDNDLSRKAVAQAPGRRYTGKRKSACTPASDHCEPLLPTSSLSIVN\nRSKEEVTSHKYQHEKLFIQVKGKKSRHQKEDSLSWSNSAYLSLDDDAFTAPFHRDGMLSL\nKQLLSFLSITDFQLPDEDFGPLKLEKVKSCSEKPVEPFESKMFGERHLKEGSCIFPEELS\nPKRMDTEMEDLEEDLIVLPGKSHPKRPNSQSQHTKTGLSSSILLYTPLNTVAPDDNDRPT\nTDMCSPAFPILGTTPAFGPQGSYEKASTEVAGRTCCTPQLAHLKDSVCLASDTKQFDSSG\nSPAKPHTTLQVSGRQGQPTCDCDSVPPGTPPPIESFTFKENQLCRNTCQELHKHSVEQTE\nTAELPASDSINPGNLQLVSELKNPSGSCSVDVSAMFWERAGCKEPCIITACEDVVSLWKA\nLDAWQWEKLYTWHFAEVPVLQIVPVPDVYNLVCVALGNLEIREIRALFCSSDDESEKQVL\nLKSGNIKAVLGLTKRRLVSSSGTLSDQQVEVMTFAEDGGGKENQFLMPPEETILTFAEVQ\nGMQEALLGTTIMNNIVIWNLKTGQLLKKMHIDDSYQASVCHKAYSEMGLLFIVLSHPCAK\nESESLRSPVFQLIVINPKTTLSVGVMLYCLPPGQAGRFLEGDVKDHCAAAILTSGTIAIW\nDLLLGQCTALLPPVSDQHWSFVKWSGTDSHLLAGQKDGNIFVYHYS",
"mw": 23.325,
"total_mw": 23.325,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "L24A monomeric mutant of PABL2. The protein construct used for SAXS contains a non-native amino acid C-terminal extension (WENLYFQS)."
}
],
"buffer": {
"name": "20 mM HEPES, 160 mM NaCl, 0.5 mM TCEP pH 7.5",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "PABL2 (Partner and localizer of BRCA2) L24A mutant",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": null,
"full_name": "Illinois Institute of Technology",
"webpage": null
}
],
"contributor_name": "Maxwell",
"contributor_surname": "Watkins",
"orcid": "https://orcid.org/0000-0003-4559-2049"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2023-12-09",
"storage_temperature": -20.0,
"cell_temperature": 23.0,
"exposure_time": 1.0,
"number_of_frames": 2199,
"wavelength": 0.1097,
"sample_detector_distance": 1.78,
"concentration_min": null,
"concentration_max": 5.1,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.083,
"s_max": 4.432,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVQ7_fit1_model1_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDVQ7_fit1_model1.pdb",
"model_mw": 23.31,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/logFile_001_1_bqXK9dm.log",
"symmetry": null,
"comment": "Model generated by SASSIE Monte Carlo, sub-ensemble selected by GAJOE (EOM/Atsas)",
"user": 941
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVQ7_fit1_model2_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDVQ7_fit1_model2.pdb",
"model_mw": 23.31,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/logFile_001_1_TvG1vcw.log",
"symmetry": null,
"comment": "Model generated by SASSIE Monte Carlo, sub-ensemble selected by GAJOE (EOM/Atsas)",
"user": 941
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVQ7_fit1_model3_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDVQ7_fit1_model3.pdb",
"model_mw": 23.31,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/logFile_001_1_lhNySOK.log",
"symmetry": null,
"comment": "Model generated by SASSIE Monte Carlo, sub-ensemble selected by GAJOE (EOM/Atsas)",
"user": 941
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVQ7_fit1_model4_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDVQ7_fit1_model4.pdb",
"model_mw": 23.31,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/logFile_001_1_ELgCP9x.log",
"symmetry": null,
"comment": "Model generated by SASSIE Monte Carlo, sub-ensemble selected by GAJOE (EOM/Atsas)",
"user": 941
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVQ7_fit1_model5_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDVQ7_fit1_model5.pdb",
"model_mw": 23.31,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/logFile_001_1_BcEA3zQ.log",
"symmetry": null,
"comment": null,
"user": 941
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVQ7_fit1_model6_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDVQ7_fit1_model6.pdb",
"model_mw": 23.31,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/logFile_001_1_x0T5g9y.log",
"symmetry": null,
"comment": "Model generated by SASSIE Monte Carlo, sub-ensemble selected by GAJOE (EOM/Atsas)",
"user": 941
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVQ7_fit1_fixed_fit_img.png",
"software": "EOM/GAJOE",
"chi_square_value": 1.395,
"p_value": 0.0017,
"fit_residual_plot": "SASDVQ7_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVQ7_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/logFile_001_1_UhvSbbF.log",
"software_version": "3.0",
"description": "Structural pool was generated using SASSIE monomer monte carlo, with residues 10-40 designated as non-flexible residues and used for structural alignment. The sub-ensemble was fit using GAJOE."
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "REGALS-separated main component profile from SEC-SAXS experiment measuring PABL2 L24A mutant. NOTE: There is a significant inconsistency between the calculated MW from sequence of the monomer (23 kDa) and the quoted experimental MW (50 kDa). CAUTION: The X-ray exposure time is unlikely to be 2199 seconds.",
"experiment_description": null,
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 49.6,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 5.136,
"pddf_i0_error": 0.05,
"guinier_i0": 5.09168,
"guinier_i0_error": null,
"pddf_rg": 5.65,
"pddf_rg_error": 0.08,
"guinier_rg": 5.23,
"guinier_rg_error": 0.888,
"pddf_dmax": 21.6,
"pddf_dmax_error": null,
"porod_volume": 127.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 21,
"guinier_point_last": 67,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDVQ7_datloglog_img.png",
"symmetry": null,
"last_modified": "2024-12-23T14:34:33.185010+01:00",
"bragg_peak": []
}
