{"code":"SASDB75","status":"Published","type_of_curve":"Single concentration","angular_unit":"1/nm","project":{"title":"VirB8 homolog TraE from plasmid pKM101 forms a hexameric ring structure and interacts with the VirB6 homolog TraD.","publication":{"title":"VirB8 homolog TraE from plasmid pKM101 forms a hexameric ring structure and interacts with the VirB6 homolog TraD.","author_list":"Casu B, Mary C, Sverzhinsky A, Fouillen A, Nanci A, Baron C","journal":"Proc Natl Acad Sci U S A","doi":"10.1073/pnas.1802501115","pmid":"29784815","published_date":"2018 Jun 5"},"status":"released","submitted_date":"2016-08-12","released_date":"2018-05-10"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDB75.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDB75.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB75_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB75_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDB75_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB75_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDB75.sascif","experiment":{"instrument":{"detector":{"type":"CCD","name":"Finger Lakes CCD","resolution":0.0},"name":"Cornell High Energy Synchrotron Source (CHESS)","city":"Ithaca, NY","country":"USA","beamline_name":"G1","beam_geometry":"","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":"Escherichia coli TraE protein (VirB8 homolog)","short_name":"TraE","sequence":"MGSSHHHHHHENLYFQGGTKANKKTGLTREAIKEFNESRKG\r\nLEVDLMDEVLKSRRTAWMVATGSAVVTVFALSLVGYVVHKYSQPIPAHLLTLNEATHEVQ\r\nQVKLTRDQTSYGDEIDKFWLTQYVIHRESYDFYSVQVDYTAVGLMSTPNVAESYQSKFKG\r\nRNGLDKVLGDSETTRVKINSVILDKPHGVATIRFTTVRRVRSNPVDDQPQRWIAIMGYEY\r\nKSLAMNAEQRYVNPLGFRVTSYRVNPEVN","organism":"Escherichia coli","uniprot_code":"Q46703","uniprot_range_first":null,"uniprot_range_last":null,"oligomerization":"hexamer","molecular_type":"protein","uniprot_sequence":"MKANKKTGLTREAIKEFNESRKGLEVDLMDEVLKSRRTAWMVATGSAVVTVFALSLVGYV\nVHKYSQPIPAHLLTLNEATHEVQQVKLTRDQTSYGDEIDKFWLTQYVIHRESYDFYSVQV\nDYTAVALMSTPNVAESYQSKFKGRNGLDKVLGDSETARVKINSVILDKPHGVRTIRFTTV\nRRVRTNPVDDQPQRWIAIMGYEYKSLAMNAEQRYVNPLGFRVTSYRVNPEVN","mw":28.537,"total_mw":171.221,"number_molecules":6,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"50 mM sodium phosphate 300 mM NaCl 40 mM imidazole 0.15 % octyl glucose neopentyl glycol (OGNG)","concentration_unit":"mM","comment":null,"additive":"300 mM NaCl, 40 mM imidazole, 0.15 % octyl glucose neopentyl glycol (OGNG)","concentration":50.0,"pka":null,"ph":7.4,"deuteration":null},"purity_method":null,"name":"Escherichia coli TraE protein: A VirB8 homolog from plasmid pKM101","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":null,"address":"Montréal, Canada","full_name":"Département de biochimie, Université de Montréal","webpage":"http://www.umontreal.ca/"}],"contributor_name":"Bastien","contributor_surname":"Casu","orcid":null}],"concentration_method":null,"concentration_unit":null,"date":"2016-06-02","storage_temperature":null,"cell_temperature":20.0,"exposure_time":2.0,"number_of_frames":70,"wavelength":null,"sample_detector_distance":null,"concentration_min":null,"concentration_max":null,"sample_volume":null,"flow_rate":null,"s_min":0.092,"s_max":2.611,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDB75_fit1_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/SASDB75_fit1_model1.pdb","model_mw":null,"bead_radius":1.9,"log":null,"symmetry":"P6","comment":"","user":144}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDB75_fit1_fit_img.png","software":null,"chi_square_value":1.16,"p_value":0.1,"fit_residual_plot":"SASDB75_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDB75_fit1.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 MW of the TraE/OGNG complex was additionally confirmed using SEC-MALLS (248kDa).","experiment_description":"X-ray synchrotron radiation scattering data from a solution of E. coli TraE protein in 50 mM sodium phosphate, 300 mM NaCl, 40 mM imidazole, 0.15 % octyl glucose neopentyl glycol (OGNG), pH 7.4 were collected using size-exclusion chromatography (SEC) SAXS on the G1 beam line at the CHESS storage ring (Ithaca, USA) using a CCD Finger Lakes CCD detector (I(s) vs s, where s = 4π sin θ/λ; 2θ is the scattering angle; λ = 0.12 nm). The data were collected as 70 successive 2 second frames through the hexameric TraE protein/OGNG elution peak and were normalized to the intensity of the transmitted beam and radially averaged. The scattering of the solvent-blank was subtracted to produce the scattering profile displayed in this entry.","tags":[],"intensity_unit":null,"experimental_mw":264.2,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":223.0,"porod_mw_error":null,"pddf_i0":0.0094,"pddf_i0_error":3e-05,"guinier_i0":0.0094,"guinier_i0_error":6e-05,"pddf_rg":4.44,"pddf_rg_error":0.013,"guinier_rg":4.44,"guinier_rg_error":0.13,"pddf_dmax":13.7,"pddf_dmax_error":null,"porod_volume":360.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":10,"guinier_point_last":35,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDB75_datloglog_img.png","symmetry":null,"last_modified":"2019-12-06T13:07:15.624532+01:00","bragg_peak":[]}