{ "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": [] }