{ "code": "SASDX42", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/nm", "project": { "title": "Biochemical and structural characterization of the human gut microbiome metallopeptidase IgAse provides insight into its unique specificity for the Fab' region of IgA1 and IgA2.", "publication": { "title": "Biochemical and structural characterization of the human gut microbiome metallopeptidase IgAse provides insight into its unique specificity for the Fab' region of IgA1 and IgA2.", "author_list": "Ramírez-Larrota JS, Juyoux P, Guerra P, Eckhard U, Gomis-Rüth FX", "journal": "PLoS Pathog", "doi": "10.1371/journal.ppat.1013292", "pmid": "40627637", "published_date": "2025 Jul" }, "status": "released", "submitted_date": "2025-02-27", "released_date": "2025-06-18" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDX42.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDX42.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX42_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX42_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDX42_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX42_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDX42.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus3 2M", "resolution": 0.172 }, "name": "ESRF", "city": "Grenoble", "country": "France", "beamline_name": "BM29", "beam_geometry": "point", "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": "IgA protease (E540A)", "short_name": "IgAse", "sequence": "MASKPDIKVGDYVKMGVYNNASILWRCVSIDNNGPLMLADKIVDTLAYDAKTNDNSNSKSHSRSYKRDDY\r\nGSNYWKDSNMRSWLNSTAAEGKVDWLCGNPPKDGYVSGVGAYNEKAGFLNAFSKSEIAAMKTVTQRSLVS\r\nHPEYNKGIVDGDANSDLLYYTDISEAVANYDSSYFETTTEKVFLLDVKQANAVWKNLKGYYVAYNNDGMA\r\nWPYWLRTPVTDCNHDMRYISSSGQVGRYAPWYSDLGVRPAFYLDSEYFVTTSGSGSQSSPYIGSAPNKQE\r\nDDYTISEPAEDANPDWNVSTEQSIQLTLGPWYSNDGKYSNPTIPVYTIQKTRSDTENMVVVVCGEGYTKS\r\nQQGKFINDVKRLWQDAMKYEPYRSYADRFNVYALCTASESTFDNGGSTFFDVIVDKYNSPVISNNLHGSQ\r\nWKNHIFERCIGPEFIEKIHDAHIKKKCDPNTIPSGSEYEPYYYVHDYIAQFAMVVNTKSDFGGAYNNREY\r\nGFHYFISPSDSYRASKTFAHAFGHGLLGLGDEYSNGYLLDDKELKSLNLSSVEDPEKIKWRQLLGFRNTY\r\nTCRNAYGSKMLVSSYECIMRDTNYQFCEVCRLQGFKRMSQLVKDVDLYVATPEVKEYTGAYSKPSDFTDL\r\nETSSYYNYTYNRNDRLLSGNSKSRFNTNMNGKKIELRTVIQNISDKNARQLKFKMWIKHSDGSVATDSSG\r\nNPLQTVQTFDIPVWNDKANFWPLGALDHIKSDFNSGLKSCSLIYQIPSDAQLKSGDTVAFQVLDENGNVL\r\nADDNTETQRYTTVSIQYKFEDGSEIPNTAGGTFTVPYGTKLDLTPAKTLYDYEFIKVDGLNKPIVSDGTV\r\nVTYYYKNKNEEHTHNLTLVAAKAATCTTAGNSAYYTCDGCDKWFADATGSVEITDKTSVKIPAPGHTAGT\r\nEWKSDDTNHWHECTVAGCGVIIESTKSAHTAGEWIVDTPATATTAGTKHKECTVCHRVLETQPIPSTGTE\r\nLKIIAGDNQIYNKASGSDVTITCNGDFAKFTGIKVDGSVVDSSNYTAVSGSTVLTLKASYLGTLTDGSHT\r\nITFVYTDGEANANLTVRTAGSGHIHDYGTEWKSNADNHWHECNCGDKKDEAAHSFKWVVDKEATATKKGS\r\nKHEECKICGYKRSAVEILEHHHHHH", "organism": "Thomasclavelia ramosa", "uniprot_code": "Q9AES2", "uniprot_range_first": 31, "uniprot_range_last": 1166, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MTKKLMTKKITAIFLALYMAISVLPMTIQAASKPDIKVGDYVKMGVYNNASILWRCVSID\nNNGPLMLADKIVDTLAYDAKTNDNSNSKSHSRSYKRDDYGSNYWKDSNMRSWLNSTAAEG\nKVDWLCGNPPKDGYVSGVGAYNEKAGFLNAFSKSEIAAMKTVTQRSLVSHPEYNKGIVDG\nDANSDLLYYTDISEAVANYDSSYFETTTEKVFLLDVKQANAVWKNLKGYYVAYNNDGMAW\nPYWLRTPVTDCNHDMRYISSSGQVGRYAPWYSDLGVRPAFYLDSEYFVTTSGSGSQSSPY\nIGSAPNKQEDDYTISEPAEDANPDWNVSTEQSIQLTLGPWYSNDGKYSNPTIPVYTIQKT\nRSDTENMVVVVCGEGYTKSQQGKFINDVKRLWQDAMKYEPYRSYADRFNVYALCTASEST\nFDNGGSTFFDVIVDKYNSPVISNNLHGSQWKNHIFERCIGPEFIEKIHDAHIKKKCDPNT\nIPSGSEYEPYYYVHDYIAQFAMVVNTKSDFGGAYNNREYGFHYFISPSDSYRASKTFAHE\nFGHGLLGLGDEYSNGYLLDDKELKSLNLSSVEDPEKIKWRQLLGFRNTYTCRNAYGSKML\nVSSYECIMRDTNYQFCEVCRLQGFKRMSQLVKDVDLYVATPEVKEYTGAYSKPSDFTDLE\nTSSYYNYTYNRNDRLLSGNSKSRFNTNMNGKKIELRTVIQNISDKNARQLKFKMWIKHSD\nGSVATDSSGNPLQTVQTFDIPVWNDKANFWPLGALDHIKSDFNSGLKSCSLIYQIPSDAQ\nLKSGDTVAFQVLDENGNVLADDNTETQRYTTVSIQYKFEDGSEIPNTAGGTFTVPYGTKL\nDLTPAKTLYDYEFIKVDGLNKPIVSDGTVVTYYYKNKNEEHTHNLTLVAAKAATCTTAGN\nSAYYTCDGCDKWFADATGSVEITDKTSVKIPAPGHTAGTEWKSDDTNHWHECTVAGCGVI\nIESTKSAHTAGEWIVDTPATATTAGTKHKECTVCHRVLETQPIPSTGTELKIIAGDNQIY\nNKASGSDVTITCNGDFAKFTGIKVDGSVVDSSNYTAVSGSTVLTLKASYLGTLTDGSHTI\nTFVYTDGEANANLTVRTAGSGHIHDYGTEWKSNADNHWHECNCGDKKDEAAHSFKWVVDK\nEATATKKGSKHEECKICGYKRSAVEIPATGTSTAPTDTTKPNDTTKPGNTNGSEKSPQTG\nDNSNIFLWFALLFVSAAGVTGITAYNKKKKEHAE", "mw": 127.857, "total_mw": 127.857, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "The protein construct used for SAXS contains an additional C-terminal polyhistidine tag (LEHHHHHH)." } ], "buffer": { "name": "50 mM Tris, 150 mM NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "IgA peptidase (A31-I1166; active site mutant E540A)", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": null, "full_name": "Molecular Biology Institute of Barcelona", "webpage": null } ], "contributor_name": "Juan Sebastián", "contributor_surname": "Ramírez Larrota", "orcid": "" } ], "concentration_method": null, "concentration_unit": null, "date": "2023-05-23", "storage_temperature": 4.0, "cell_temperature": 20.0, "exposure_time": 4.0, "number_of_frames": 250, "wavelength": 0.099, "sample_detector_distance": 2.867, "concentration_min": null, "concentration_max": 4.0, "sample_volume": null, "flow_rate": null, "s_min": 0.063, "s_max": 5.21, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDX42_fit1_model1_img.png", "software": "EOM/RANCH", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDX42_fit1_model1.cif", "model_mw": null, "bead_radius": 1.9, "log": null, "symmetry": null, "comment": "0.44 volume fraction", "user": 1196 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDX42_fit1_model2_img.png", "software": "EOM/RANCH", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDX42_fit1_model2.cif", "model_mw": null, "bead_radius": 1.9, "log": null, "symmetry": null, "comment": "0.11 volume fraction", "user": 1196 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDX42_fit1_model3_img.png", "software": "EOM/RANCH", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDX42_fit1_model3.cif", "model_mw": null, "bead_radius": 1.9, "log": null, "symmetry": null, "comment": "0.11 volume fraction", "user": 1196 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDX42_fit1_model4_img.png", "software": "EOM/RANCH", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDX42_fit1_model4.cif", "model_mw": null, "bead_radius": 1.9, "log": null, "symmetry": null, "comment": "0.22 volume fraction", "user": 1196 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDX42_fit1_model5_img.png", "software": "EOM/RANCH", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDX42_fit1_model5.cif", "model_mw": null, "bead_radius": 1.9, "log": null, "symmetry": null, "comment": "0.11 volume fraction", "user": 1196 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDX42_fit1_fixed_fit_img.png", "software": "EOM/GAJOE", "chi_square_value": 1.541, "p_value": 0.0139, "fit_residual_plot": "SASDX42_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDX42_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/logFile_001_1_9MVb3vS.log", "software_version": "2.1", "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": "The results obtained from EOM analysis are made available in the full entry zip archive.", "experiment_description": "Synchrotron SAXS data from solutions of IgA peptidase in 50 mM Tris, 150 mM NaCl, pH 8 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus3 2M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.099 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 4.00 mg/ml was measured at 20°C. 250 successive 4 second frames were collected. 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": 118.8, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 119.0, "porod_mw_error": null, "pddf_i0": 72.97, "pddf_i0_error": null, "guinier_i0": 70.169, "guinier_i0_error": null, "pddf_rg": 6.433, "pddf_rg_error": null, "guinier_rg": 5.65, "guinier_rg_error": 0.035, "pddf_dmax": 27.9, "pddf_dmax_error": null, "porod_volume": 190.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 6, "guinier_point_last": 33, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDX42_datloglog_img.png", "symmetry": null, "last_modified": "2025-07-21T18:12:24.155654+02:00", "bragg_peak": [] }