{ "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": [] }