{"code":"SASDFC6","status":"Published","type_of_curve":"SEC-SAS","angular_unit":"1/nm","project":{"title":"Studying Conformational Changes of the Yersinia Type-III-Secretion Effector YopO in Solution by Integrative Structural Biology.","publication":{"title":"Studying Conformational Changes of the Yersinia Type-III-Secretion Effector YopO in Solution by Integrative Structural Biology.","author_list":"Peter MF, Tuukkanen AT, Heubach CA, Selsam A, Duthie FG, Svergun DI, Schiemann O, Hagelueken G","journal":"Structure","doi":"10.1016/j.str.2019.06.007","pmid":"31303480","published_date":"2019 Sep 3"},"status":"released","submitted_date":"2019-05-06","released_date":"2019-09-11"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDFC6.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDFC6.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFC6_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFC6_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFC6_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFC6_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDFC6.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":"Protein kinase YopO","short_name":"YopO","sequence":"KPQTELPLGWKGKPLSGAPDLEGMRVAHISIIERLVAKIGHLFAELEAYKHIYKTAGKHPNLANVHGMAVVPYGNRYYYALLMDEVDGWRCSDTLRSLADSWKQGKINSEAYWGTIKFIAHRLLDVTNHLAKAGIVHNDIKPGNVVFDRASGEPVVIDLGLHSRSGEQPKGFTESFKAPELGVGGASEKSDVFLVVSTLLHGIEGFEKDPEIKPNQGLRFITSEPAHVMDENGYPIHRPGIAGVETAYTRFITDILGVSADSRPDSNEARLHEFLSDGTIDEESAKQILKDTLTGEMSITPYYLRELSDLLRTHLSSAATKQLDMGVVLSDLDTMLVALDKAEREGGVDKDQLKSFNSLILKTYSVIGAYILSIVEPSLQRIQKHLDQTHSFSDIGSLMRAHKHLETLLEVLVTLSQQGQPVSSETYSFLNRLAEAKVTLSQQLNTLQQQQESAKAQLSILINRSGSWADVARQSLQRFDSTRPVVKFGTEQYTAIHRQMMAAHAAITLQEVSEFTDDMRNFTADSIPLLIQLGRSSLMDEHLVEQREKLRELTTIAERLNRLEREWM","organism":"Yersinia enterocolitica","uniprot_code":"Q93KQ6","uniprot_range_first":89,"uniprot_range_last":729,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MKIMGTMSPSISLAKAHERISKHWQNPVGELNIEGKRYRIIDNQVLRLNPHSGFSLFREG\nVGKIFSGKMFSFSIARNLTDTLHAAQKTTSQELRSDIPNALSNLFGAKPQTELPLGWKGK\nPLSGAPDLEGMRVAETDKFAEGESHISIIETKDKQRLVAKIERSIAEGHLFAELEAYKHI\nYKTAGKHPNLANVHGMAVVPYGNRKEEALLMDEVDGWRCSDTLRSLADSWKQGKINSEAY\nWGTIKFIAHRLLDVTNHLAKAGIVHNDIKPGNVVFDRASGEPVVIDLGLHSRSGEQPKGF\nTESFKAPELGVGNLGASEKSDVFLVVSTLLHGIEGFEKDPEIKPNQGLRFITSEPAHVMD\nENGYPIHRPGIAGVETAYTRFITDILGVSADSRPDSNEARLHEFLSDGTIDEESAKQILK\nDTLTGEMSPLPTDVRRITPKKLRELSDLLRTHLSSAATKQLDMGVVLSDLDTMLVALDKA\nEREGGVDKDQLKSFNSLILKTYSVIGAYIKGREGDTKSSSTEVSPYHRSNFMLSIVEPSL\nQRIQKHLDQTHSFSDIGSLMRAHKHLETLLEVLVTLSQQGQPVSSETYSFLNRLAEAKVT\nLSQQLNTLQQQQESAKAQLSILINRSGSWADVARQSLQRFDSTRPVVKFGTEQYTAIHRQ\nMMAAHAAITLQEVSEFTDDMRNFTADSIPLLIQLGRSSLMDEHLVEQREKLRELTTIAER\nLNRLEREWM","mw":63.387,"total_mw":63.387,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"10 mM Tris-HCl, 50 mM NaCl","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":8.0,"deuteration":null},"purity_method":null,"name":"Wild type protein kinase YopO","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":"Anne","contributor_surname":"Tuukkanen","orcid":null}],"concentration_method":null,"concentration_unit":null,"date":"2017-05-06","storage_temperature":10.0,"cell_temperature":20.0,"exposure_time":1.0,"number_of_frames":3600,"wavelength":0.124,"sample_detector_distance":3.0,"concentration_min":null,"concentration_max":5.52,"sample_volume":80.0,"flow_rate":null,"s_min":0.111,"s_max":7.267,"total_exposure_time":null,"seccolumn":1},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDFC6_fit1_model1_img.png","software":"Custom in-house","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDFC6_fit1_model1.pdb","model_mw":63.35,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":27}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/combine_apo_01_fixed_fit_img.png","software":"CRYSOL","chi_square_value":0.979,"p_value":0.1027,"fit_residual_plot":"combine_apo_01_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDFC6_fit1.fit","fit_log":null,"software_version":null,"description":""}],"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 protein kinase YopO in 10 mM Tris-HCl, 50 mM NaCl, pH 8 were collected on the EMBL P12 beam line at the 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 (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAXS was employed. The SEC parameters were as follows: A 80 μl sample at 5.5 mg/ml was injected onto a GE Superdex 200 Increase 10/300 column at 20°C. 3600 successive 1 second frames were collected through the SEC elution. The data from the sample peak were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.","tags":[],"intensity_unit":"arbitrary","experimental_mw":68.8,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":66.2,"porod_mw_error":null,"pddf_i0":270.0,"pddf_i0_error":1.4,"guinier_i0":267.5,"guinier_i0_error":0.7,"pddf_rg":3.419,"pddf_rg_error":null,"guinier_rg":3.34,"guinier_rg_error":0.1,"pddf_dmax":11.45,"pddf_dmax_error":0.6,"porod_volume":119.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":2,"guinier_point_last":102,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDFC6_datloglog_img.png","symmetry":null,"last_modified":"2023-06-21T07:56:39.492710+02:00","bragg_peak":[]}