{ "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": [] }