{"code":"SASDD45","status":"Published","type_of_curve":"SEC-SAS","angular_unit":"1/A","project":{"title":"The molecular basis of protein toxin HicA-dependent binding of the protein antitoxin HicB to DNA.","publication":{"title":"The molecular basis of protein toxin HicA-dependent binding of the protein antitoxin HicB to DNA.","author_list":"Winter AJ, Williams C, Isupov MN, Crocker H, Gromova M, Marsh P, Wilkinson OJ, Dillingham MS, Harmer NJ, Titball RW, Crump MP","journal":"J Biol Chem","doi":"10.1074/jbc.RA118.005173","pmid":"30337369","published_date":"2018 Oct 18"},"status":"released","submitted_date":"2018-03-17","released_date":"2018-11-03"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDD45_revised.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDD45.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD45_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD45_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDD45_revised_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD45_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDD45.sascif","experiment":{"instrument":{"detector":{"type":null,"name":"Pilatus 2M","resolution":null},"name":"Diamond Light Source","city":"Didcot","country":"UK","beamline_name":"B21","beam_geometry":"1 x 5 mm","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":"Type II toxin-antitoxin system HicB family antitoxin","short_name":"HicB","sequence":"MMEFPIAVHKDDGSVYGVTVPDIPGVHSWGETIDDAIKNTREAIVGHVETLIELGEDVEF\r\nTCSTVEELVAKPEYAGAVWALVSVDLSQLDSKPERINVSIPRFVLHKIDAYVASRHETRS\r\nGFLARAALEALNEGKKHHHHHH","organism":"Burkholderia pseudomallei","uniprot_code":"Q63NA5","uniprot_range_first":1,"uniprot_range_last":134,"oligomerization":"tetramer","molecular_type":"protein","uniprot_sequence":"MEFPIAVHKDDGSVYGVTVPDIPGVHSWGETIDDAIKNTREAIVGHVETLIELGEDVEFT\nCSTVEELVAKPEYAGAVWALVSVDLSQLDSKPERINVSIPRFVLHKIDAYVASRHETRSG\nFLARAALEALNEGKVRHA","mw":15.739,"total_mw":62.956,"number_molecules":4,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"25 mM Tris, 150 mM NaCl","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":7.5,"deuteration":null},"purity_method":null,"name":"Type II toxin-antitoxin system HicB family antitoxin - HicB protein","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":null,"address":"Bristol, UK","full_name":"University of Bristol","webpage":"http://www.bristol.ac.uk"}],"contributor_name":"Ash","contributor_surname":"Winter","orcid":null}],"concentration_method":null,"concentration_unit":null,"date":"2016-07-28","storage_temperature":4.0,"cell_temperature":25.0,"exposure_time":3.0,"number_of_frames":null,"wavelength":0.1,"sample_detector_distance":4.014,"concentration_min":null,"concentration_max":5.0,"sample_volume":null,"flow_rate":null,"s_min":0.04,"s_max":4.075,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDD45_fit1_model1_img.png","software":"PyMOL","pdb_link":[{"pdb_code":"6g1n","ext_code":"6G1N","ext_type":"pdb","difference_with_model":"identical"}],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDD45_fit1_model1.pdb","model_mw":57.95,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":296}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD45_fit1_fitfoxs_img.png","software":"FoXS","chi_square_value":1.975269,"p_value":0.0,"fit_residual_plot":"SASDD45_fit1_fitfoxsresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDD45_fit1.dat","fit_log":null,"software_version":null,"description":null}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"5","i0_calibration_standard":null,"description":"Analysis of the data involved ScÅtter (www.bioisis.net/). The resultant curve was fit with the crystal structure of HicB, PDB Code: 6G1N.","experiment_description":"Synchrotron SAXS data from solutions of HicB protein in 25 mM Tris 150 mM NaCl, pH 7.5, were collected using in-line SEC-SAXS at the B21 beam line at the Diamond Light Source (Oxfordshire, UK) using a Pilatus 2M detector at a sample-detector distance of 4.0 m and at a wavelength of λ = 0.1 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In line SEC-SAXS was performed using an Agilent 1200 HPLC system equipped with a 2.4 mL Superdex S200 column (GE Healthcare). A sample concentration of 5mg/ml was loaded onto the column at a flow rate of 0.04 mL/min. Data frames were collected at 25°C for the entire column elution with an exposure time of 3 seconds per frame through an angular s-range of 0.04-4 nm-1. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted using data frames measured from the flow-through column buffer with no macromolecular sample present.","tags":[],"intensity_unit":"arbitrary","experimental_mw":62.0,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":70.0,"porod_mw_error":null,"pddf_i0":0.003825,"pddf_i0_error":5e-05,"guinier_i0":0.00380685,"guinier_i0_error":1e-05,"pddf_rg":3.098,"pddf_rg_error":0.06,"guinier_rg":3.04,"guinier_rg_error":0.056,"pddf_dmax":10.5,"pddf_dmax_error":null,"porod_volume":112.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":35,"guinier_point_last":121,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDD45_datloglog_img.png","symmetry":null,"last_modified":"2020-05-08T08:19:46.838764+02:00","bragg_peak":[]}