{"code":"SASDUY5","status":"Published","type_of_curve":"SEC-SAS","angular_unit":"1/nm","project":{"title":"Structural Basis for Membrane Targeting and Secretion of Legionella SidE Ubiquitin Ligases","publication":null,"status":"released","submitted_date":"2024-03-29","released_date":"2025-11-19"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDUY5.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDUY5.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUY5_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUY5_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDUY5_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUY5_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDUY5.sascif","experiment":{"instrument":{"detector":{"type":null,"name":"Pilatus 6M","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":"Ubiquitinating/deubiquitinating enzyme SdeA","short_name":null,"sequence":"GSDFSDVEKLEQQIQVIDTKLADAYLLEVTKQISALDNTKPKNQTELKTKIAAFLDRTTDIEMLRNERIKKHGSSKDPLDLSDLDKLSGSLQRINQSLVSDLITTIRVSINQMEAKTFHEQEKEIQQNFELLAKLEKTLDKSKTSEKLREDIPKLNDLLVAKQKAYPQMVQMQLKSEVFVTQLREVCQANHDDLDKTRNARLRELDRLDREAGITRMVGNLIWGLTNKVGLTTDERLDIRTKQQSLARFKNELFNDKIDTDQLISNLARKRPSELQEGLGISTDNAMELHLLLTELAGKTTSPDELEERMKAIDDISTKIGREPEHLKFVMVEEDESNKKTIGF","organism":"Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)","uniprot_code":"Q5ZTK4","uniprot_range_first":1158,"uniprot_range_last":1499,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MPKYVEGVELTQEGMHAIFARMGYGDITSGSIYNGVPTIDTGALNRQGFMPVLTGVGPHR\nDSGHWIMLIKGPGNQYYLFDPLGKTSGEGYQNILAAQLPMGSTLSVIPNGSGLNMGLCGY\nWVASAGLRAHQALNQHNPPTLLNVGQTITNEMRNELDHDGYRKITGWLRAVADEFPEGDP\nQLDGKALRENTEKDLKIEIPTLVLPGKDTSPKEMSVKPTAPQDKSVPVWNGFSLYTDDTV\nKAAAQYAYDNYLGKPYTGSVESAPANFGGRMVYRQHHGLSHTLRTMAYAELIVEEARKAK\nLRGETLGKFKDGRTIADVTPQELKKIMIAQAFFVAGRDDEASDAKNYQKYHEQSRDAFLK\nYVKDNESTLIPDVFKDQEDVNFYARVIEDKSHDWESTPAHVLINQGHMVDLVRVKQPPES\nFLQRYFSSMQRWIGSQATEAVFGIQRQFFHATYEVVAGFDSDNKEPHLVVSGLGRYVIGE\nDGQPIREAPKKGQKEGDLKVFPQTYKLKENERLMRVDEFLKLPEIQNTFPGSGKHLQGGM\nPGMNEMDYWNRLNSLNRARCENDVDFCLKQLQTAHDKAKIEPIKQAFQSSKGKERRQPNV\nDEIAAARIIQQILANPDCIHDDHVLINGQKLEQQFFRDLLAKCEMAVVGSLLNDTDIGNI\nDTLMRHEKDTEFHSTNPEAVPVKIGEYWINDQRINNSSGNITQKKHDLIFLMQNDAWYFS\nRVNAIAQNRDKGSTFKEVLITTLMTPLTSKALVDTSQAKPPTRLFRGLNLSEEFTKGLID\nQANAMIANTTERLFTDHSPEAFKQIKLNDLSKMSGRTNASTTTEIKLVKETWDSNVIFEM\nLDPDGLLHSKQVGRHGEGTESEFSVYLPEDVALVPVKVTLDGKTQKGENRYVFTFVAVKS\nPDFTPRHESGYAVEPFLRMQAAKLAEVKSSIEKAQRAPDLETIFNLQNEVEAVQYSHLST\nGYKNFLKNTVGPVLENSLSGLMESDTDTLSKALAAFPSDTQWSAFNFEEARQAKRQMDAI\nKQMVGNKVVLDALTQCQDALEKQNIAGALDALKKIPSEKEMGTIRRELREQIQSARQELE\nSLQRAVVTPVVTDEKKVRERYDALIENTSKKITELETGKLPNLDAVKKGISNLSNLKQEV\nTVLRNEKIRMHVGTDKVDFSDVEKLEQQIQVIDTKLADAYLLEVTKQISALDNTKPKNQT\nELKTKIAAFLDRTTDIEMLRNERIKKHGSSKDPLDLSDLDKLSGSLQRINQSLVSDLITT\nIRVSINQMEAKTFHEQEKEIQQNFELLAKLEKTLDKSKTSEKLREDIPKLNDLLVAKQKA\nYPQMVQMQLKSEVFVTQLREVCQANHDDLDKTRNARLRELDRLDREAGITRMVGNLIWGL\nTNKVGLTTDERLDIRTKQQSLARFKNELFNDKIDTDQLISNLARKRPSELQEGLGISTDN\nAMELHLLLTELAGKTTSPDELEERMKAIDDISTKIGREPEHLKFVMVEEDESNKKTIGF","mw":39.388,"total_mw":39.388,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":"Protein construct used for SAXS contains an additional two non-native amino acids at N-terminus (GS)."},{"long_name":"Type 4 adapter protein IcmS","short_name":null,"sequence":"MGSSHHHHHHSQDPMERDISKCMAKIAASMNAKFYLNDRFVSFDEVFSETGLLPAIAKRADQLCSLCLGYGLGATYDESEGALLGIRVVFDEVTPNVLRLLCMTDVMNELIQGGPSRDYTPLDEL","organism":"Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)","uniprot_code":"Q5ZYD0","uniprot_range_first":1,"uniprot_range_last":111,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MERDISKCMAKIAASMNAKFYLNDRFVSFDEVFSETGLLPAIAKRADQLCSLCLGYGLGA\nTYDESEGALLGIRVVFDEVTPNVLRLLCMTDVMNELIQGGPSRDYTPLDELMYD","mw":13.876,"total_mw":13.876,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":"The protein construct used for SAXS contains an additional non-native amino acid extension at the N-terminus (MGSSHHHHHHSQDP)."},{"long_name":"Type 4 adapter protein IcmW (S9A)","short_name":null,"sequence":"MPDLSHEAAAKYWFEYLDPMIYRVITFMESVENWTLDGNPELEEAMKQLGQELDDIEKIDLGLLAEEDKFIRIVGNIKSGRGLRLLQAIDTVHPGSASRVLIHAEETSLSSSDPAGFFLKRNIVFERLRLLSRVFCQYRLKLVLRALEGDE","organism":"Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)","uniprot_code":"Q5ZS31","uniprot_range_first":1,"uniprot_range_last":151,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MPDLSHEASAKYWFEYLDPMIYRVITFMESVENWTLDGNPELEEAMKQLGQELDDIEKID\nLGLLAEEDKFIRIVGNIKSGRGLRLLQAIDTVHPGSASRVLIHAEETSLSSSDPAGFFLK\nRNIVFERLRLLSRVFCQYRLKLVLRALEGDE","mw":17.313,"total_mw":17.313,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":""},{"long_name":"Type 4 coupling protein DotL","short_name":null,"sequence":"MGQNEPEPVEDIVEEEVEGALTIFSKLRIDPNAPPILVADKEVFSEPLLPINETRNQMITIERLAGAKDKYAGTVANELIKDFQIATSYPPEERDVIDVQELTGIIRDLSAKISAEREKANKKAAEELTLEHHHHHH","organism":"Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)","uniprot_code":"Q5ZYC6","uniprot_range_first":656,"uniprot_range_last":783,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MMRGIDSRHELDPTLLLRDTRTFTQRLADFFADPTNISIVLISLAAVSYYFSEAATFLLI\nMGGIFFLYSYTRKQKLPFRLPQISRAKDYNDLKPGINKPNIARGITFFGNDRKTGEELWF\nANDDMRTHALIFGSTGSGKTETLVSLSYNALVQGSGFIYVDGKGDNSLYAKVFSMVRSMG\nREDDLLLINFMTGARDIVGPQEKRLSNTLNPFCQGSSSMLTQLVVSLMGSSGQSSDGDMW\nKGRAIAFVEALMRLLVYMRDEGAILLDANTIRNYFDLQRLESIVIDKVFPRDDQESVNIE\nTIPKLVTDPLRNYLNTLPGYNKEKKGKQVSQVLEQHGFITMQLVRSFSSLADTYGHIIRT\nNLAEVDFKDVVLNRRILVVLLPALEKSPDELSNLGKIIVSSLKAMMAAGLGEEVEGDYRD\nVILRKPTNAPTPYMCILDEYGYYAVQGFAVVPAQARSLGFSAIFAGQDLPAFQKASKEEA\nASIGANTNIKICMKLEDPTETWDFFTKTAGEAYVTKVDSFQTKETSIANSYMDTKSSSFE\nKRARVDLLDLKEQTEGEAHIFFKSKIVRARMFYANPKPVKQLKINQFLKVEPPPDDYLMK\nLQKQLASFQSILESGDLSINKAVENEEITLISKALKESTIVEPIERGVAALIAFHGQNEP\nEPVEDIVEEEVEGALTIFSKLRIDPNAPPILVADKEVFSEPLLPINETRNQMITIERLAG\nAKDKYAGTVANELIKDFQIATSYPPEERDVIDVQELTGIIRDLSAKISAEREKANKKAAE\nELT","mw":15.397,"total_mw":15.397,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":"The protein construct used for SAXS contains a polyhistidine tag at the N-terminus (LEHHHHHH)."}],"buffer":{"name":"25 mM Tris-HCl, 200 mM NaCl, 5 mM DTT","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":7.5,"deuteration":null},"purity_method":null,"name":"C-terminal domain of Ubiquitinating/deubiquitinating enzyme SdeA bound to Type 4 adaptor protein complex IcmS, IcmW and DotL (SdeACTD-IcmSWDotLc complex)","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":"Ahmed","contributor_surname":"Mohammed","orcid":""}],"concentration_method":null,"concentration_unit":null,"date":"2020-12-04","storage_temperature":25.0,"cell_temperature":25.0,"exposure_time":1.0,"number_of_frames":37,"wavelength":0.124,"sample_detector_distance":3.0,"concentration_min":null,"concentration_max":9.0,"sample_volume":95.0,"flow_rate":0.7,"s_min":0.114,"s_max":4.314,"total_exposure_time":null,"seccolumn":3},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDUY5_fit1_model1_img.png","software":"SREFLEX","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDUY5_fit1_model1.pdb","model_mw":78.34,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":700}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDUY5_fit1_fixed_fit_img.png","software":"SREFLEX","chi_square_value":1.348,"p_value":0.0014,"fit_residual_plot":"SASDUY5_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDUY5_fit1.fit","fit_log":null,"software_version":null,"description":""},{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDUY5_fit2_model1_img.png","software":"MONSA","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":"1.45 (r12592)","model_data":"https://www.sasbdb.org/media/pdb_file/SASDUY5_fit2_model1.pdb","model_mw":null,"bead_radius":4.25,"log":null,"symmetry":null,"comment":null,"user":700}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDUY5_fit2_fixed_fit_img.png","software":"MONSA","chi_square_value":1.299,"p_value":4e-05,"fit_residual_plot":"SASDUY5_fit2_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDUY5_fit2.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 the SdeA_CTD-IcmSWDotLc complex in 25 mM Tris-HCl, 200 mM NaCl, 5 mM DTT, pH 7.5 were collected on the EMBL P12 beam line at PETRA III (DESY; Hamburg, Germany) using a Pilatus 6M 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) SAS was employed. The SEC parameters were as follows: A 95.00 μl sample at 9 mg/ml was injected at a 0.70 ml/min flow rate onto a GE Superdex 75 Increase 10/300 column at 25°C. 37 successive 1 second frames were collected through the main SEC elution peak. The data 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":83.0,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":116.0,"porod_mw_error":null,"pddf_i0":41870.0,"pddf_i0_error":null,"guinier_i0":41548.1,"guinier_i0_error":null,"pddf_rg":3.944,"pddf_rg_error":0.01,"guinier_rg":3.839,"guinier_rg_error":0.02,"pddf_dmax":14.4,"pddf_dmax_error":null,"porod_volume":166.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":12,"guinier_point_last":81,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDUY5_datloglog_img.png","symmetry":null,"last_modified":"2025-11-19T15:45:33.381484+01:00","bragg_peak":[]}