{ "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": [] }