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{
"code": "SASDEU3",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "Senescence-associated ubiquitin ligase 1 (SAUL1)",
"publication": null,
"status": "released",
"submitted_date": "2017-07-21",
"released_date": "2021-09-13"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEU3.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEU3.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEU3_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEU3_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEU3_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEU3_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEU3.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 2M",
"resolution": null
},
"name": "PETRA III",
"city": "DESY; Hamburg",
"country": "Germany",
"beamline_name": "EMBL P12",
"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": "Senescence-associated E3 ubiquitin ligase 1",
"short_name": "SAUL1",
"sequence": "GPLGS\r\nMVGSSDGDQSDDSSHFERGVDHIYEAFICPLTKEVMHDPVTLENGRTFEREAIEKWFKEC\r\nRDSGRPPSCPLTSQELTSTDVSASIALRNTIEEWRSRNDAAKLDIARQSLFLGNAETDIL\r\nQALMHVRQICRTIRSNRHGVRNSQLIHMIIDMLKSTSHRVRYKALQTLQVVVEGDDESKA\r\nIVAEGDTVRTLVKFLSHEPSKGREAAVSLLFELSKSEALCEKIGSIHGALILLVGLTSSN\r\nSENVSIVEKADRTLENMERSEEIVRQMASYGRLQPLLGKLLEGSPETKLSMASFLGELPL\r\nNNDVKVLVAQTVGSSLVDLMRSGDMPQREAALKALNKISSFEGSAKVLISKGILPPLIKD\r\nLFYVGPNNLPIRLKEVSATILANIVNIGYDFDKATLVSENRVENLLHLISNTGPAIQCKL\r\nLEVLVGLTSCPKTVPKVVYAIKTSGAIISLVQFIEVRENDDLRLASIKLLHNLSPFMSEE\r\nLAKALCGTAGQLGSLVAIISEKTPITEEQAAAAGLLAELPDRDLGLTQEMLEVGAFEKII\r\nSKVFGIRQGDIKGMRFVNPFLEGLVRILARITFVFNKEARAINFCREHDVASLFLHLLQS\r\nNGQDNIQMVSAMALENLSLESIKLTRMPDPPPVNYCGSIFSCVRKPHVVNGLCKIHQGIC\r\nSLRETFCLVEGGAVEKLVALLDHENVKVVEAALAALSSLLEDGLDVEKGVKILDEADGIR\r\nHILNVLRENRTERLTRRAVWMVERILRIEDIAREVAEEQSLSAALVDAFQNADFRTRQIA\r\nENALKHIDKIPNFSSIFPNIA",
"organism": "Arabidopsis thaliana",
"uniprot_code": "Q9LM76",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "tetramer",
"molecular_type": "protein",
"uniprot_sequence": "MVGSSDGDQSDDSSHFERGVDHIYEAFICPLTKEVMHDPVTLENGRTFEREAIEKWFKEC\nRDSGRPPSCPLTSQELTSTDVSASIALRNTIEEWRSRNDAAKLDIARQSLFLGNAETDIL\nQALMHVRQICRTIRSNRHGVRNSQLIHMIIDMLKSTSHRVRYKALQTLQVVVEGDDESKA\nIVAEGDTVRTLVKFLSHEPSKGREAAVSLLFELSKSEALCEKIGSIHGALILLVGLTSSN\nSENVSIVEKADRTLENMERSEEIVRQMASYGRLQPLLGKLLEGSPETKLSMASFLGELPL\nNNDVKVLVAQTVGSSLVDLMRSGDMPQREAALKALNKISSFEGSAKVLISKGILPPLIKD\nLFYVGPNNLPIRLKEVSATILANIVNIGYDFDKATLVSENRVENLLHLISNTGPAIQCKL\nLEVLVGLTSCPKTVPKVVYAIKTSGAIISLVQFIEVRENDDLRLASIKLLHNLSPFMSEE\nLAKALCGTAGQLGSLVAIISEKTPITEEQAAAAGLLAELPDRDLGLTQEMLEVGAFEKII\nSKVFGIRQGDIKGMRFVNPFLEGLVRILARITFVFNKEARAINFCREHDVASLFLHLLQS\nNGQDNIQMVSAMALENLSLESIKLTRMPDPPPVNYCGSIFSCVRKPHVVNGLCKIHQGIC\nSLRETFCLVEGGAVEKLVALLDHENVKVVEAALAALSSLLEDGLDVEKGVKILDEADGIR\nHILNVLRENRTERLTRRAVWMVERILRIEDIAREVAEEQSLSAALVDAFQNADFRTRQIA\nENALKHIDKIPNFSSIFPNIA",
"mw": 88.79,
"total_mw": 355.16,
"number_molecules": 4,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Glutathione S-transferase",
"short_name": "GST",
"sequence": "MSPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELGLEFPNLPYYIDGD\r\nVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVLDIRYGVSRIAYSKDFETLKVDFLS\r\nKLPEMLKMFEDRLCHKTYLNGDHVTHPDFMLYDALDVVLYMDPMCLDAFPKLVCFKKRIEAI\r\nPQIDKYLKSSKYIAWPLQGWQATFGGGDHPPKSD\r\nLEVLFQ",
"organism": "Schistosoma japonicum",
"uniprot_code": "P08515",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "tetramer",
"molecular_type": "protein",
"uniprot_sequence": "MSPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELGLEFPNLPYYID\nGDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVLDIRYGVSRIAYSKDFETLKV\nDFLSKLPEMLKMFEDRLCHKTYLNGDHVTHPDFMLYDALDVVLYMDPMCLDAFPKLVCFK\nKRIEAIPQIDKYLKSSKYIAWPLQGWQATFGGGDHPPK",
"mw": 26.43,
"total_mw": 105.72,
"number_molecules": 4,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "50 mM Tris, 250 mM NaCl",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 9.0,
"deuteration": null
},
"purity_method": null,
"name": "GST-SAUL1",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Hamburg, Germany",
"full_name": "University of Hamburg",
"webpage": "https://www.uni-hamburg.de/"
}
],
"contributor_name": "Haifa",
"contributor_surname": "El Kilani",
"orcid": null
},
{
"affiliation": [
{
"short_name": "EMBL-Hamburg",
"address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
"full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
"webpage": "http://www.embl-hamburg.de/index.php"
}
],
"contributor_name": "Al",
"contributor_surname": "Kikhney",
"orcid": "https://orcid.org/0000-0003-1321-3956"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2014-01-20",
"storage_temperature": 20.0,
"cell_temperature": 23.0,
"exposure_time": 0.05,
"number_of_frames": 20,
"wavelength": 0.123956,
"sample_detector_distance": 3.0,
"concentration_min": null,
"concentration_max": 1.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.02,
"s_max": 4.509,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEU3_fit1_model1_img.png",
"software": "CORAL",
"pdb_link": [
{
"pdb_code": "3bby",
"ext_code": "3BBY",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "mix",
"software_version": "05",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEU3_fit1_model1.pdb",
"model_mw": 462.3,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/manual_iBfc9IX.log",
"symmetry": "P222",
"comment": "",
"user": 4
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEU3_fit1_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 0.682,
"p_value": 0.950757,
"fit_residual_plot": "SASDEU3_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEU3_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/manual00.log",
"software_version": "2.8.3",
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEU3_fit2_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEU3_fit2_model1.pdb",
"model_mw": 491.0,
"bead_radius": 6.1,
"log": null,
"symmetry": "P222",
"comment": "",
"user": 4
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEU3_fit2_fixed_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 0.72,
"p_value": 0.321151,
"fit_residual_plot": "SASDEU3_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEU3_fit2.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/gstsaulp_6_5.log",
"software_version": "r9450",
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "The rigid bodies used for the SAUL1 tetramer model were predicted by I-TASSER.",
"experiment_description": null,
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 486.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 486.0,
"porod_mw_error": null,
"pddf_i0": 1720.0,
"pddf_i0_error": null,
"guinier_i0": 1734.36,
"guinier_i0_error": null,
"pddf_rg": 7.762,
"pddf_rg_error": 0.148,
"guinier_rg": 7.63,
"guinier_rg_error": 0.96,
"pddf_dmax": 28.0,
"pddf_dmax_error": null,
"porod_volume": 778.34,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 9,
"guinier_point_last": 53,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDEU3_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}
