{"code":"SASDF24","status":"Published","type_of_curve":"SEC-SAS","angular_unit":"1/nm","project":{"title":"Conformational characterization of full-length X-chromosome-linked inhibitor of apoptosis protein (XIAP) through an integrated approach.","publication":{"title":"Conformational characterization of full-length X-chromosome-linked inhibitor of apoptosis protein (XIAP) through an integrated approach.","author_list":"Polykretis P, Luchinat E, Bonucci A, Giachetti A, Graewert MA, Svergun DI, Banci L","journal":"IUCrJ","doi":"10.1107/S205225251901073X","pmid":"31576227","published_date":"2019 Sep 1"},"status":"released","submitted_date":"2019-03-14","released_date":"2019-08-28"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDF24.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDF24.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF24_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF24_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDF24_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF24_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDF24.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":"E3 ubiquitin-protein ligase XIAP","short_name":null,"sequence":"MTFNSFEGSKTCVPADINKEEEFVEEFNRLKTFANFPSGSPVSASTLARAGFLYTGEGDT\r\nVRCFSCHAAVDRWQYGDSAVGRHRKVSPNCRFINGFYLENSATQSTNSGIQNGQYKVENY\r\nLGSRDHFALDRPSETHADYLLRTGQVVDISDTIYPRNPAMYSEEARLKSFQNWPDYAHLT\r\nPRELASAGLYYTGIGDQVQCFCCGGKLKNWEPCDRAWSEHRRHFPNCFFVLGRNLNIRSE\r\nSDAVSSDRNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKC\r\nFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLEECLVRTTEKTP\r\nSLTRRIDDTIFQNPMVQEAIRMGFSFKDIKKIMEEKIQISGSNYKSLEVLVADLVNAQKD\r\nSMQDESSQTSLQKEISTEEQLRRLQEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEAVDK\r\nCPMCYTVITFKQKIFMS","organism":"Homo sapiens","uniprot_code":"P98170","uniprot_range_first":1,"uniprot_range_last":497,"oligomerization":"dimer","molecular_type":"protein","uniprot_sequence":"MTFNSFEGSKTCVPADINKEEEFVEEFNRLKTFANFPSGSPVSASTLARAGFLYTGEGDT\nVRCFSCHAAVDRWQYGDSAVGRHRKVSPNCRFINGFYLENSATQSTNSGIQNGQYKVENY\nLGSRDHFALDRPSETHADYLLRTGQVVDISDTIYPRNPAMYSEEARLKSFQNWPDYAHLT\nPRELASAGLYYTGIGDQVQCFCCGGKLKNWEPCDRAWSEHRRHFPNCFFVLGRNLNIRSE\nSDAVSSDRNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKC\nFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLEECLVRTTEKTP\nSLTRRIDDTIFQNPMVQEAIRMGFSFKDIKKIMEEKIQISGSNYKSLEVLVADLVNAQKD\nSMQDESSQTSLQKEISTEEQLRRLQEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEAVDK\nCPMCYTVITFKQKIFMS","mw":56.684,"total_mw":113.368,"number_molecules":2,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"Xiap buffer","concentration_unit":null,"comment":"20 mM Tris buffer, 0.5 mM TCEP,","additive":null,"concentration":null,"pka":null,"ph":7.4,"deuteration":null},"purity_method":null,"name":"Full-length X-chromosome linked inhibitor of apoptosis protein (XIAP)","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"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":"Melissa ","contributor_surname":"Graewert","orcid":null}],"concentration_method":null,"concentration_unit":null,"date":"2017-09-15","storage_temperature":null,"cell_temperature":20.0,"exposure_time":1.0,"number_of_frames":15,"wavelength":0.124,"sample_detector_distance":3.0,"concentration_min":null,"concentration_max":7.5,"sample_volume":null,"flow_rate":null,"s_min":0.091,"s_max":5.064,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDF24_fit1_model1_img.png","software":"HADDOCK","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDF24_fit1_model1.pdb","model_mw":114.0,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":14}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/testGR1_372700_fixed_fit_img.png","software":"CRYSOL","chi_square_value":1.528,"p_value":5.3e-05,"fit_residual_plot":"testGR1_372700_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDF24_fit1.fit","fit_log":null,"software_version":null,"description":"A number of models were gennerated using HADDOCK (van Zundert, G. C. P. et al. The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. J. Mol. Biol. 428, 720–725 (2016).\r\nThese were screened against the SAXS data using Crysol. The model with the best fit is shown here.\r\nModel input: starting from the atomic structures of the individual domains: BIR1 (2POI.pdb), BIR2 (1I3O.pdb), BIR3 (5M6E.pdb), UBA (2KNA.pdb) and RING (5O6T.pdb)."}],"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 X-chromosome linked inhibitor of apoptosis protein (XIAP) in Xiap buffer, pH 7.4 were collected using size-exclusion chromatography SAXS (SEC-SAXS) on the EMBL P12 beam line at PETRA III (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 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: Superdex 200 10/300 GL (GE healthcare Life Sciences); Flow rate: 0.5 mL/min; Sample injection concentration: 7.5 mg/mL; Injection volume: 100 μL. The data were collected through the SEC peak of the protein as a series of 15 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":115.0,"experimental_mw_error":null,"guinier_i0_mw":0.0,"guinier_i0_mw_error":null,"porod_mw":130.0,"porod_mw_error":null,"pddf_i0":16800.0,"pddf_i0_error":null,"guinier_i0":16438.0,"guinier_i0_error":32.0,"pddf_rg":3.99,"pddf_rg_error":null,"guinier_rg":3.86,"guinier_rg_error":0.06,"pddf_dmax":12.82,"pddf_dmax_error":null,"porod_volume":207.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":34,"guinier_point_last":89,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDF24_datloglog_img.png","symmetry":null,"last_modified":"2023-06-21T07:56:39.492710+02:00","bragg_peak":[]}