{ "code": "SASDFU3", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/nm", "project": { "title": "A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex.", "publication": { "title": "A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex.", "author_list": "Marabelli C, Marrocco B, Pilotto S, Chittori S, Picaud S, Marchese S, Ciossani G, Forneris F, Filippakopoulos P, Schoehn G, Rhodes D, Subramaniam S, Mattevi A", "journal": "Cell Rep", "doi": "10.1016/j.celrep.2019.03.061", "pmid": "30970244", "published_date": "2019 Apr 9" }, "status": "released", "submitted_date": "2019-03-12", "released_date": "2019-04-16" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFU3.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFU3.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFU3_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFU3_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFU3_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFU3_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFU3.sascif", "experiment": { "instrument": { "detector": { "type": "Dectris", "name": "Pilatus 1M", "resolution": 172.0 }, "name": "ESRF", "city": "Grenoble", "country": "France", "beamline_name": "BM29", "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": "Lysyne-specific Demethylase LSD2", "short_name": "LSD2", "sequence": "KKKATETTDEDEDGGSEKKYRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEH\r\nFCNECFDHYYRSHKDGYDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPECRKW\r\nRQLTKEIQLTPQIAKTYRCGMKPNTAIKPETSDHCSLPEDLRVLEVSNHWWYSMLILPPL\r\nLKDSVAAPLLSAYYPDCVGMSPSCTSTNRAAATGNASPGKLEHSKAALSVHVPGMNRYFQ\r\nPFYQPNECGKALCVRPDVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEALTPQK\r\nCIPHIIVRGLVRIRCVQEVERILYFMTRKGLINTGVLSVGADQYLLPKDYHNKSVIIIGA\r\nGPAGLAAARQLHNFGIKVTVLEAKDRIGGRVWDDKSFKGVTVGRGAQIVNGCINNPVALM\r\nCEQLGISMHKFGERCDLIQEGGRITDPTIDKRMDFHFNALLDVVSEWRKDKTQLQDVPLG\r\nEKIEEIYKAFIKESGIQFSELEGQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAG\r\nDHTLLTPGYSVIIEKLAEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVTVPLA\r\nLLQKGAIQFNPPLSEKKMKAINSLGAGIIEKIALQFPYRFWDSKVQGADFFGHVPPSASK\r\nRGLFAVFYDMDPQKKHSVLMSVIAGEAVASVRTLDDKQVLQQCMATLRELFKEQEVPDPT\r\nKYFVTRWSTDPWIQMAYSFVKTGGSGEAYDIIAEDIQGTVFFAGEATNRHFPQTVTGAYL\r\nSGVREASKIAAF", "organism": "Homo sapiens", "uniprot_code": "Q8NB78", "uniprot_range_first": 31, "uniprot_range_last": 822, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MATPRGRTKKKASFDHSPDSLPLRSSGRQAKKKATETTDEDEDGGSEKKYRKCEKAGCTA\nTCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECFDHYYRSHKDGYDKYTTWKKIWTSN\nGKTEPSPKAFMADQQLPYWVQCTKPECRKWRQLTKEIQLTPQIAKTYRCGMKPNTAIKPE\nTSDHCSLPEDLRVLEVSNHWWYSMLILPPLLKDSVAAPLLSAYYPDCVGMSPSCTSTNRA\nAATGNASPGKLEHSKAALSVHVPGMNRYFQPFYQPNECGKALCVRPDVMELDELYEFPEY\nSRDPTMYLALRNLILALWYTNCKEALTPQKCIPHIIVRGLVRIRCVQEVERILYFMTRKG\nLINTGVLSVGADQYLLPKDYHNKSVIIIGAGPAGLAAARQLHNFGIKVTVLEAKDRIGGR\nVWDDKSFKGVTVGRGAQIVNGCINNPVALMCEQLGISMHKFGERCDLIQEGGRITDPTID\nKRMDFHFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESGIQFSELEGQVLQFHL\nSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLLTPGYSVIIEKLAEGLDIQLKSPVQC\nIDYSGDEVQVTTTDGTGYSAQKVLVTVPLALLQKGAIQFNPPLSEKKMKAINSLGAGIIE\nKIALQFPYRFWDSKVQGADFFGHVPPSASKRGLFAVFYDMDPQKKHSVLMSVIAGEAVAS\nVRTLDDKQVLQQCMATLRELFKEQEVPDPTKYFVTRWSTDPWIQMAYSFVKTGGSGEAYD\nIIAEDIQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAAF", "mw": 88.832, "total_mw": 88.832, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "15 mM HEPES, 200 mM NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.3, "deuteration": null }, "purity_method": null, "name": "Lysine-specific Demethylase (LSD2)", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Italy", "full_name": "University of Pavia", "webpage": "http://wcm-3.unipv.it" } ], "contributor_name": "Federico", "contributor_surname": "Forneris", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2017-12-11", "storage_temperature": 4.0, "cell_temperature": 20.0, "exposure_time": 1.0, "number_of_frames": 167, "wavelength": 0.1, "sample_detector_distance": 2.87, "concentration_min": null, "concentration_max": 2.0, "sample_volume": null, "flow_rate": null, "s_min": 0.057, "s_max": 2.852, "total_exposure_time": null, "seccolumn": null }, "fits": [], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of lysine-specific demethylase (LSD2) in 15 mM HEPES, 200 mM NaCl, pH 7.3 were collected using size-exclusion chromatography SAXS (SEC-SAXS) on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.1 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). SEC-SAXS was performed at 20 °C using the following parameters: Column: Wyatt WTC-030N5; Flow rate: 0.25 mL/min; Sample injection concentration: 3 mg/mL; Injection volume: 50 μL. The data were collected through the SEC peak of the sample as a series of 167 x 1 second exposures. Each unsubtracted data frame was normalised to the intensity of the transmitted beam and radially averaged and the scattering of an appropriate solvent-blank was subtracted. The resulting subtracted frames were scaled and averaged to generate the final SAXS profile displayed in this entry.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 89.8, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 78.0, "porod_mw_error": null, "pddf_i0": 27.01, "pddf_i0_error": null, "guinier_i0": 26.89, "guinier_i0_error": 0.1, "pddf_rg": 3.405, "pddf_rg_error": null, "guinier_rg": 3.36, "guinier_rg_error": 0.01, "pddf_dmax": 10.59, "pddf_dmax_error": null, "porod_volume": 124.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 15, "guinier_point_last": 74, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDFU3_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }