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{
"code": "SASDE37",
"status": "Published",
"type_of_curve": "Other",
"angular_unit": "1/A",
"project": {
"title": "Molecular architecture of the Jumonji C family histone demethylase KDM5B.",
"publication": {
"title": "Molecular architecture of the Jumonji C family histone demethylase KDM5B.",
"author_list": "Dorosz J, Kristensen LH, Aduri NG, Mirza O, Lousen R, Bucciarelli S, Mehta V, Sellés-Baiget S, Solbak SMØ, Bach A, Mesa P, Hernandez PA, Montoya G, Nguyen TTTN, Rand KD, Boesen T, Gajhede M",
"journal": "Sci Rep",
"doi": "10.1038/s41598-019-40573-y",
"pmid": "30858420",
"published_date": "2019 Mar 11"
},
"status": "released",
"submitted_date": "2018-10-29",
"released_date": "2019-03-15"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDE37.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDE37.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDE37_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDE37_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDE37_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDE37_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDE37.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "pixel counting",
"name": "Pilatus3 R 300K",
"resolution": 172.0
},
"name": "University of Copenhagen, Department of Drug Design and Pharmacology",
"city": "Copenhagen",
"country": "Denmark",
"beamline_name": "Xenocs BioXolver L with GeniX3D",
"beam_geometry": null,
"type_of_source": "X-ray in house",
"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": "Lysine-specific demethylase 5B",
"short_name": "KDM5B",
"sequence": "MEAATTLHPGPRPALPLGGPGPLGEFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTG\r\nICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLNFLDQIAKYWELQGSTLKI\r\nPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKAVGSHIRGHYERILN\r\nPYNLFLSGDSLRCLQKPNLTTDTKDKEYKPHDIPQRQSVQPSETCPPARRAKRMRAEAMN\r\nIKIEPEETTEARTHNLRRRMGCPTPKCENEKEMKSSIKQEPIERKDYIVENEKEKPKSRS\r\nKKATNAVDLYVCLLCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKCLAQE\r\nCSKPQEAFGFEQAARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEED\r\nVTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADIC\r\nGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPE\r\nLFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAV\r\nNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIE\r\nDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVK\r\nELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAESYNEWALNVNEALEAKINKKKSLVSFK\r\nALIEESEMKKFPDNDLLRHLRLVTQDAEKCASVAQQLLNGKRQTRYRSGGGKSQNQLTVN\r\nELRQFVTQLYALPCVLSQTPLLKDLLNRVEDFQQHSQKLLSEETPSAAELQDLLDVSFEF\r\nDVELPQLAEMRIRLEQARWLEEVQQACLDPSSLTLDDMRRLIDLGVGLAPYSAVEKAMAR\r\nGPLQELLTVSEHWDDKAKSLLKARPRHSLNSLATAVKEIEEIPAYLPNGAALKDSVQRARDW\r\nLQDVEGLQAGGRVPVLDTLIELVTRGRSIPVHLNSLPRLETLVAEVQAWKECAVNTFLTE\r\nNSPYSLLEVLCPRCDIGLLGLKRKQRKLKEPLPNGKKKSTKLESLSDLERALTESKETAS\r\nAMATLGEARLREMEALQSLRLANEGKLLSPLQDVDIKICLCQKAPAAPMIQCELCRDAFH\r\nTSCVAVPSISQGLRIWLCPHCRRSEKPPLEKILPLLASLQRIRVRLPEGDALRYMIERTV\r\nNWQHRAQQLLSSGNLKFVQDRVGSGLLYSRWQASAGQVSDTNKVSQPPGTTSFSLPDDWD\r\nNRTSYLHSPFSTGRSCIPLHGVSPEVNELLMEAQLLQVSLPEIQELYQTLLAKPSPAQQT\r\nDRSSPVRPSSEKNDCCRGKRDGINSLERKLKRRLEREGLSSERWERVKKMRTPKKKKIKL\r\nSHPKDMNNFKLERERSYELVRSAETHSLPSDTSYSEQEDSEDEDAICPAVSCLQPEGDEV\r\nDWVQCDGSCNQWFHQVCVGVSPEMAEKEDYICVRCTVKDAPSRK",
"organism": "Homo sapiens",
"uniprot_code": "Q9UGL1",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MEAATTLHPGPRPALPLGGPGPLGEFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTG\nICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLNFLDQIAKYWELQGSTLKI\nPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKAVGSHIRGHYERILN\nPYNLFLSGDSLRCLQKPNLTTDTKDKEYKPHDIPQRQSVQPSETCPPARRAKRMRAEAMN\nIKIEPEETTEARTHNLRRRMGCPTPKCENEKEMKSSIKQEPIERKDYIVENEKEKPKSRS\nKKATNAVDLYVCLLCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKCLAQE\nCSKPQEAFGFEQAARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEED\nVTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADIC\nGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPE\nLFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAV\nNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIE\nDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVK\nELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAESYNEWALNVNEALEAKINKKKSLVSFK\nALIEESEMKKFPDNDLLRHLRLVTQDAEKCASVAQQLLNGKRQTRYRSGGGKSQNQLTVN\nELRQFVTQLYALPCVLSQTPLLKDLLNRVEDFQQHSQKLLSEETPSAAELQDLLDVSFEF\nDVELPQLAEMRIRLEQARWLEEVQQACLDPSSLTLDDMRRLIDLGVGLAPYSAVEKAMAR\nLQELLTVSEHWDDKAKSLLKARPRHSLNSLATAVKEIEEIPAYLPNGAALKDSVQRARDW\nLQDVEGLQAGGRVPVLDTLIELVTRGRSIPVHLNSLPRLETLVAEVQAWKECAVNTFLTE\nNSPYSLLEVLCPRCDIGLLGLKRKQRKLKEPLPNGKKKSTKLESLSDLERALTESKETAS\nAMATLGEARLREMEALQSLRLANEGKLLSPLQDVDIKICLCQKAPAAPMIQCELCRDAFH\nTSCVAVPSISQGLRIWLCPHCRRSEKPPLEKILPLLASLQRIRVRLPEGDALRYMIERTV\nNWQHRAQQLLSSGNLKFVQDRVGSGLLYSRWQASAGQVSDTNKVSQPPGTTSFSLPDDWD\nNRTSYLHSPFSTGRSCIPLHGVSPEVNELLMEAQLLQVSLPEIQELYQTLLAKPSPAQQT\nDRSSPVRPSSEKNDCCRGKRDGINSLERKLKRRLEREGLSSERWERVKKMRTPKKKKIKL\nSHPKDMNNFKLERERSYELVRSAETHSLPSDTSYSEQEDSEDEDAICPAVSCLQPEGDEV\nDWVQCDGSCNQWFHQVCVGVSPEMAEKEDYICVRCTVKDAPSRK",
"mw": 175.81,
"total_mw": 175.81,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "50 mM HEPES, 300 mM NaCl, 5% (v/v) glycerol, 1mM DTT",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.7,
"deuteration": null
},
"purity_method": null,
"name": "Lysine-specific demethylase 5B, KDM5B, in HEPES buffer",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Copenhagen, Denmark",
"full_name": "University of Copenhagen",
"webpage": "http://www.ku.dk/"
}
],
"contributor_name": "Saskia",
"contributor_surname": "Bucciarelli",
"orcid": "https://orcid.org/0000-0001-7612-223X"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2018-10-24",
"storage_temperature": 7.0,
"cell_temperature": 7.0,
"exposure_time": null,
"number_of_frames": null,
"wavelength": 0.154,
"sample_detector_distance": null,
"concentration_min": 0.75,
"concentration_max": 1.8,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.056,
"s_max": 4.829,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDE37_fit1_model1_img.png",
"software": "DAMFILT",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDE37_fit1_model1.pdb",
"model_mw": 188.971,
"bead_radius": 4.75,
"log": "https://www.sasbdb.org/media/log_files/KDM5B_damsel_ODluz3B.log",
"symmetry": "P1",
"comment": "Averaged Spatial Repersentation",
"user": 365
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDE37_fit1_model2_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "r9988",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDE37_fit1_model2.pdb",
"model_mw": 188.0,
"bead_radius": 2.4,
"log": "https://www.sasbdb.org/media/log_files/KDM5B_01.log",
"symmetry": "P1",
"comment": "Individual model",
"user": 365
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/KDM5B_01_gWRh3qa_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 2.098,
"p_value": 0.736543,
"fit_residual_plot": "KDM5B_01_gWRh3qa_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDE37_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/KDM5B_01_qMSueUo.log",
"software_version": null,
"description": "DAMMIF was run in slow mode"
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "KDM5B at concentrations of 0.75, 1, 1.5 and 1.8 mg/ml were measured with two different sample-detector distances (d1 = 571 mm, d2 = 1382 mm) using a sample volume of 7 µl per concentration. After background correction, the scattering curves were brought to absolute scale using water as a secondary standard and subsequently normalized by concentration. As no concentration-dependence was observed, all four curves were then averaged to produce the current data set. Measurement times were:\r\n0.75 mg/ml: d1: 90 min, d2: 120 min;\r\n1 mg/ml: d1: 60 min, d2: 120 min;\r\n1.5 mg/ml: d1: 60 min, d2: 100 min;\r\n1.8 mg/ml: d1: 30 min, d2: 40 min. The dummy atom model (top) represents the spatially aligned and volume occupancy corrected low resolution structure obtained from multiple shape reconstructions (DAMFILT model) that are available in the full entry zip archive. An individual model example (bottom) and the corresponding fit to the data are also displayed.",
"experiment_description": "SAXS data from solutions of lysine-specific demethylase 5B, KDM5B, in 50 mM HEPES, 300 mM NaCl, 5% (v/v) glycerol, 1mM DTT, pH 7.7 were collected on a Xenocs / BioXolver L GeniX3D instrument at the University of Copenhagen, Department of Drug Design and Pharmacology (Copenhagen, Denmark) using a Pilatus3 R 300K detector at a wavelength of λ = 0.154 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.8 and 1.8 mg/ml were measured at 7°C.",
"tags": [],
"intensity_unit": "1/cm",
"experimental_mw": 121.0,
"experimental_mw_error": null,
"guinier_i0_mw": 152.0,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 0.06685,
"pddf_i0_error": null,
"guinier_i0": 0.08391,
"guinier_i0_error": 0.0113,
"pddf_rg": 8.53,
"pddf_rg_error": null,
"guinier_rg": 8.841,
"guinier_rg_error": 3.342,
"pddf_dmax": 26.9,
"pddf_dmax_error": null,
"porod_volume": null,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 10,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDE37_datloglog_img.png",
"symmetry": null,
"last_modified": "2021-08-18T17:30:30.308210+02:00",
"bragg_peak": []
}
