{"code":"SASDV54","status":"Published","type_of_curve":"SEC-SAS","angular_unit":"1/nm","project":{"title":"Structural-function relationship of YdaS, a Cro-type repressor in the cryptic prophage CP-933P from Escherichia coli O157:H7","publication":null,"status":"released","submitted_date":"2024-07-01","released_date":"2024-07-30"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDV54.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDV54.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDV54_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDV54_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDV54_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDV54_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDV54.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":"Phage antirepressor protein Cro","short_name":"YdaS protein","sequence":"MTLKEFIKSLRVGDAKKFAARLGVSPSYLSQMASGRTAISPTRALMIESATEGQVSRAELRPHDWELIWPEYASGIRLGQTHVVHAEGDCSACLSDGVDSGSSHHHHHH","organism":"Escherichia coli O157:H7","uniprot_code":"Q8XAD7","uniprot_range_first":1,"uniprot_range_last":100,"oligomerization":"dimer","molecular_type":"protein","uniprot_sequence":"MTLKEFIKSLRVGDAKKFAARLGVSPSYLSQMASGRTAISPTRALMIESATEGQVSRAEL\nRPHDWELIWPEYASGIRLGQTHVVHAEGDCSACLSDGVDS","mw":11.902,"total_mw":23.804,"number_molecules":2,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":"Phage antirepressor protein Cro. The protein construct used for SAXS contains an additional non-native polyhistidine tag at the C-terminus (GSSHHHHHH)."},{"long_name":"IR1 22 base pair dsDNA","short_name":"IR1","sequence":"TTGTTTAGTGATTACTAAAGAT\r\nAACAAATCACTAATGATTTCTA","organism":null,"uniprot_code":null,"uniprot_range_first":null,"uniprot_range_last":null,"oligomerization":"monomer","molecular_type":"DNA","uniprot_sequence":"","mw":13.606,"total_mw":13.606,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":""}],"buffer":{"name":"20 mM sodium acetate, 150 mM NaCl, 1 mM TCEP","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":5.5,"deuteration":null},"purity_method":null,"name":"YdaS, a cro-type repressor from Escherichai coli O157:H7 cryptic prophage CP-933 bound to a 22 base pair dsDNA.","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":"VUB","address":"Pleinlaan 2 1050 Brussel ","full_name":"Vrije Universiteit Brussel","webpage":"http://www.vub.ac.be/"}],"contributor_name":"Marusa","contributor_surname":"Prolic Kalinsek","orcid":"https://orcid.org/0000-0003-4175-1858"}],"concentration_method":null,"concentration_unit":null,"date":"2021-04-13","storage_temperature":null,"cell_temperature":15.0,"exposure_time":null,"number_of_frames":null,"wavelength":0.0992,"sample_detector_distance":2.81,"concentration_min":null,"concentration_max":15.0,"sample_volume":45.0,"flow_rate":0.16,"s_min":0.044,"s_max":5.205,"total_exposure_time":null,"seccolumn":34},"fits":[{"models":[{"model_plot":null,"software":"Other [static image]","pdb_link":[],"model_title":null,"type_of_model":"other","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDV54_fit1_model1.png","model_mw":null,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":9}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDV54_fit1_fixed_fit_img.png","software":"Other","chi_square_value":1.2621,"p_value":0.0148,"fit_residual_plot":"SASDV54_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDV54_fit1.saxs","fit_log":null,"software_version":"calcSAXS","description":""}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"5.0","i0_calibration_standard":null,"description":"The atomic coordinates of the full model ensemble are made available in the full entry zip archive. X-ray exposure time = UNKNOWN. Number of sample data frames = UNKNOWN.","experiment_description":"Synchrotron SAXS data from solutions of YdaS, a cro-type repressor from Escherichai coli O157:H7 cryptic prophage CP-933 bound to a 22 base pair dsDNA in 20 mM sodium acetate, 150 mM NaCl, 1 mM TCEP, pH 5.5 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus3 2M detector at a sample-detector distance of 2.8 m and at a wavelength of λ = 0.0992 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 45.00 μl sample at 15 mg/ml was injected at a 0.16 ml/min flow rate onto a Agilent AdvanceBio SEC 300Å, 4.6 x 150 mm column at 15°C. 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":35.4,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":null,"porod_mw_error":null,"pddf_i0":140.7,"pddf_i0_error":null,"guinier_i0":140.401,"guinier_i0_error":null,"pddf_rg":2.898,"pddf_rg_error":null,"guinier_rg":2.84,"guinier_rg_error":0.009,"pddf_dmax":10.12,"pddf_dmax_error":null,"porod_volume":52.95,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":21,"guinier_point_last":76,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDV54_datloglog_img.png","symmetry":null,"last_modified":"2024-07-30T18:06:40.919061+02:00","bragg_peak":[]}