{"code":"SASDB95","status":"Published","type_of_curve":"Other","angular_unit":"1/nm","project":{"title":"The Shigella Virulence Factor IcsA Relieves N-WASP Autoinhibition by Displacing the Verprolin Homology/Cofilin/Acidic (VCA) Domain.","publication":{"title":"The Shigella Virulence Factor IcsA Relieves N-WASP Autoinhibition by Displacing the Verprolin Homology/Cofilin/Acidic (VCA) Domain.","author_list":"Mauricio RP, Jeffries CM, Svergun DI, Deane JE","journal":"J Biol Chem","doi":"10.1074/jbc.M116.758003","pmid":"27881679","published_date":"2017 Jan 6"},"status":"released","submitted_date":"2016-08-17","released_date":"2016-11-24"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDB95.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDB95.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB95_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB95_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDB95_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB95_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDB95.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":"Outer membrane protein IcsA (53-758)","short_name":"IcsA","sequence":"TPLSGTQELHFSEDNYEKLLTPVDGLSPLGAGEDGMDAWYITSSNPSH\r\nASRTKLRINSDIMISAGHGGAGDNNDGNSCGGNGGDSITGSDLSIINQGM\r\nILGGSGGSGADHNGDGGEAVTGDNLFIINGEIISGGHGGDSYSDSDGGNG\r\nGDAVTGVNLPIINKGTISGGNGGNNYGEGDGGNGGDAITGSSLSVINKGT\r\nFAGGNGGAAYGYGYDGYGGNAITGDNLSVINNGAILGGNGGHWGDAINGS\r\nNMTIANSGYIISGKEDDGTQNVAGNAIHITGGNNSLILHEGSVITGDVQV\r\nNNSSILKIINNDYTGTTPTIEGDLCAGDCTTVSLSGNKFTVSGDVSFGEN\r\nSSLNLAGISSLEASGNMSFGNNVKVEAIINNWAQKDYKLLSADKGITGFS\r\nVSNISIINPLLTTGAIDYTKSYISDQNKLIYGLSWNDTDGDSHGEFNLKE\r\nNAELTVSTILADNLSHHNINSWDGKSLTKSGEGTLILAEKNTYSGFTNIN\r\nAGILKMGTVEAMTRTAGVIVNKGATLNFSGMNQTVNTLLNSGTVLINNIN\r\nAPFLPDPVIVTGNMTLEKNGHVILNNSSSNVGQTYVQKGNWHGKGGILSL\r\nGAVLGNDNSKTDRLEIAGHASGITYVAVTNEGGSGDKTLEGVQIISTDSS\r\nDKNAFIQKGRIVAGSYDYRLKQGTVSGLNTNKWYLTSQMDNQESKQMSNQ\r\nESTQMSSR","organism":"Shigella flexneri","uniprot_code":"Q7BCK4","uniprot_range_first":null,"uniprot_range_last":null,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MNQIHKFFCNMTQCSQGGAGELPTVKEKTCKLSFSPFVVGASLLLGGPIAFATPLSGTQE\nLHFSEDNYEKLLTPVDGLSPLGAGEDGMDAWYITSSNPSHASRTKLRINSDIMISAGHGG\nAGDNNDGNSCGGNGGDSITGSDLSIINQGMILGGSGGSGADHNGDGGEAVTGDNLFIING\nEIISGGHGGDSYSDSDGGNGGDAVTGVNLPIINKGTISGGNGGNNYGEGDGGNGGDAITG\nSSLSVINKGTFAGGNGGAAYGYGYDGYGGNAITGDNLSVINNGAILGGNGGHWGDAINGS\nNMTIANSGYIISGKEDDGTQNVAGNAIHITGGNNSLILHEGSVITGDVQVNNSSILKIIN\nNDYTGTTPTIEGDLCAGDCTTVSLSGNKFTVSGDVSFGENSSLNLAGISSLEASGNMSFG\nNNVKVEAIINNWAQKDYKLLSADKGITGFSVSNISIINPLLTTGAIDYTKSYISDQNKLI\nYGLSWNDTDGDSHGEFNLKENAELTVSTILADNLSHHNINSWDGKSLTKSGEGTLILAEK\nNTYSGFTNINAGILKMGTVEAMTRTAGVIVNKGATLNFSGMNQTVNTLLNSGTVLINNIN\nAPFLPDPVIVTGNMTLEKNGHVILNNSSSNVGQTYVQKGNWHGKGGILSLGAVLGNDNSK\nTDRLEIAGHASGITYVAVTNEGGSGDKTLEGVQIISTDSSDKNAFIQKGRIVAGSYDYRL\nKQGTVSGLNTNKWYLTSQMDNQESKQMSNQESTQMSSRRASSQLVSSLNLGEGSIHTWRP\nEAGSYIANLIAMNTMFSPSLYDRHGSTIVDPTTGQLSETTMWIRTVGGHNEHNLADRQLK\nTTANRMVYQIGGDILKTNFTDHDGLHVGIMGAYGYQDSKTHNKYTSYSSRGTVSGYTAGL\nYSSWFQDEKERTGLYMDAWLQYSWFNNTVKGDGLTGEKYSSKGITGALEAGYIYPTIRWT\nAHNNIDNALYLNPQVQITRHGVKANDYIEHNGTMVTSSGGNNIQAKLGLRTSLISQSCID\nKETLRKFEPFLEVNWKWSSKQYGVIMNGMSNHQIGNRNVIELKTGVGGRLADNLSIWGNV\nSQQLGNNSYRDTQGILGVKYTF","mw":72.476,"total_mw":72.476,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"50 mM Tris 150 mM NaCl 10 mM CaCl2 3% v/v glycerol","concentration_unit":"mM","comment":null,"additive":"150 mM NaCl, 10 mM CaCl2, 3% v/v glycerol","concentration":50.0,"pka":null,"ph":7.4,"deuteration":null},"purity_method":null,"name":"Shigella outer membrane protein IcsA autotransporter","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":"CIMR","address":"Cambridge, UK","full_name":"Cambridge Institute for Medical Research , Department of Pathology, University of Cambridge","webpage":"http://www.cimr.cam.ac.uk/"}],"contributor_name":"Janet","contributor_surname":"Deane","orcid":null},{"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":"Cy M","contributor_surname":"Jeffries","orcid":null},{"affiliation":[{"short_name":"CIMR","address":"Cambridge, UK","full_name":"Cambridge Institute for Medical Research , Department of Pathology, University of Cambridge","webpage":"http://www.cimr.cam.ac.uk/"}],"contributor_name":"Rui","contributor_surname":"Mauricio","orcid":null}],"concentration_method":null,"concentration_unit":null,"date":"2016-05-18","storage_temperature":20.0,"cell_temperature":20.0,"exposure_time":1.0,"number_of_frames":119,"wavelength":0.124,"sample_detector_distance":3.1,"concentration_min":null,"concentration_max":null,"sample_volume":null,"flow_rate":null,"s_min":0.076,"s_max":3.009,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDB95_fit1_model1_img.png","software":"DAMMIN","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":"","model_data":"https://www.sasbdb.org/media/pdb_file/SASDB95_fit1_model1.pdb","model_mw":63.1,"bead_radius":3.4,"log":"https://www.sasbdb.org/media/log_files/IcsA1a.log","symmetry":"","comment":"","user":9}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDB95_fit1_fit_img.png","software":null,"chi_square_value":1.858,"p_value":0.841,"fit_residual_plot":"SASDB95_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDB95_fit1.fir","fit_log":null,"software_version":null,"description":null},{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDB95_fit2_model1_img.png","software":"GASBOR","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":"","model_data":"https://www.sasbdb.org/media/pdb_file/SASDB95_fit2_model1.pdb","model_mw":null,"bead_radius":1.9,"log":"https://www.sasbdb.org/media/log_files/Ic_Ga9.log","symmetry":"","comment":"","user":9}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDB95_fit2_fit_img.png","software":null,"chi_square_value":1.86,"p_value":0.841,"fit_residual_plot":"SASDB95_fit2_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDB95_fit2.fir","fit_log":null,"software_version":null,"description":null}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":null,"i0_calibration_standard":null,"description":"The bead models displayed for IcsA are individual/representative low-resolution structural examples calculated using DAMMIN or GASBOR. A cohort of individual GASBOR and DAMMIN models are supplied in the full entry zip archive and include the average DAMMIN-based spatial representation of IcsA in solution (damfilt.pdb; NSD = 0.7).\r\nIndividual reduced SEC-SAXS data frames/blocks and Rg/I(0) analysis through the IcsA elution peak are included in the full entry zip archive.","experiment_description":"Synchrotron SAXS data from solutions of Shigella flexneri outer membrane protein IcsA (53–758) in 50 mM Tris, 150 mM NaCl, 10 mM CaCl2, 3% v/v glycerol, pH 7.4 were collected using size-exclusion chromatography (SEC) SAXS on the EMBL-P12 bioSAXS beam line at the PETRAIII storage ring (Hamburg, Germany) equipped with a Pilatus 2M detector (I(s) vs s, where s = 4π sin θ/λ; 2θ is the scattering angle; λ = 0.124 nm). 119 successive 1 second frames were collected through the monomeric IcsA SEC elution peak (GE Healthcare Life Sciences Superdex 200 Increase column; 0.4 ml/min; 75 μl injection at 8 mg/ml). The data were normalised to the intensity of the transmitted beam and the scattering of the solvent-blank (derived from 50 x 1 s data frames of pure, macromolecular free solvent) was subtracted. The resulting scattering profiles were scaled relative to each other (CorMap p > 0.01) then averaged to produce the final averaged IcsA SAXS data displayed in this entry.","tags":[],"intensity_unit":null,"experimental_mw":65.0,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":65.0,"porod_mw_error":null,"pddf_i0":0.7582,"pddf_i0_error":0.0022,"guinier_i0":0.75,"guinier_i0_error":0.0022,"pddf_rg":3.76,"pddf_rg_error":0.02,"guinier_rg":3.65,"guinier_rg_error":0.02,"pddf_dmax":13.22,"pddf_dmax_error":null,"porod_volume":103.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":6,"guinier_point_last":102,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDB95_datloglog_img.png","symmetry":null,"last_modified":"2023-06-21T07:56:39.492710+02:00","bragg_peak":[]}