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{
"code": "SASDUX5",
"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/SASDUX5.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDUX5.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUX5_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUX5_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDUX5_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUX5_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDUX5.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": "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": "Type 4 adaptor protein complex IcmS, IcmW and DotL (IcmS/IcmW/DotLc)",
"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": 34,
"wavelength": 0.124,
"sample_detector_distance": 3.0,
"concentration_min": null,
"concentration_max": 10.0,
"sample_volume": 100.0,
"flow_rate": 0.7,
"s_min": 0.111,
"s_max": 5.092,
"total_exposure_time": null,
"seccolumn": 3
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDUX5_fit1_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/SASDUX5_fit1_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/SASDUX5_fit1_fixed_fit_img.png",
"software": "MONSA",
"chi_square_value": 1.088,
"p_value": 0.6239,
"fit_residual_plot": "SASDUX5_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDUX5_fit1.fit",
"fit_log": null,
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDUX5_fit2_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/SASDUX5_fit2_model1.pdb",
"model_mw": 40.36,
"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/SASDUX5_fit2_fixed_fit_img.png",
"software": "SREFLEX",
"chi_square_value": 1.221,
"p_value": 0.0001,
"fit_residual_plot": "SASDUX5_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDUX5_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 IcmS/IcmW/DotLc 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 100.00 μl sample at 10 mg/ml was injected at a 0.70 ml/min flow rate onto a GE Superdex 75 Increase 10/300 column at 25°C. 34 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": 42.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 44.0,
"porod_mw_error": null,
"pddf_i0": 17790.0,
"pddf_i0_error": null,
"guinier_i0": 17733.1,
"guinier_i0_error": null,
"pddf_rg": 2.795,
"pddf_rg_error": null,
"guinier_rg": 2.758,
"guinier_rg_error": 0.006,
"pddf_dmax": 9.61,
"pddf_dmax_error": null,
"porod_volume": 71.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 2,
"guinier_point_last": 130,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDUX5_datloglog_img.png",
"symmetry": null,
"last_modified": "2025-11-19T15:45:32.267458+01:00",
"bragg_peak": []
}
