{"code":"SASDDD8","status":"Published","type_of_curve":"Single concentration","angular_unit":"1/nm","project":{"title":"M. tuberculosis class II apurinic/ apyrimidinic-endonuclease/3'-5' exonuclease (XthA) engages with NAD+-dependent DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision repair.","publication":{"title":"M. tuberculosis class II apurinic/ apyrimidinic-endonuclease/3'-5' exonuclease (XthA) engages with NAD+-dependent DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision repair.","author_list":"Khanam T, Afsar M, Shukla A, Alam F, Kumar S, Soyar H, Dolma K, Pasupuleti M, Srivastava KK, Ampapathi RS, Ramachandran R","journal":"Nucleic Acids Res","doi":"10.1093/nar/gkaa188","pmid":"32232338","published_date":"2020 Mar 30"},"status":"released","submitted_date":"2018-09-06","released_date":"2019-05-28"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDDD8.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDDD8.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDD8_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDD8_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDD8_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDD8_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDDD8.sascif","experiment":{"instrument":{"detector":{"type":"Dectris","name":"Pilatus 1M","resolution":172.0},"name":"ESRF","city":"Grenoble","country":"France","beamline_name":"BM29","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":"Probable exodeoxyribonuclease III protein XthA","short_name":"MtbXthA","sequence":"MPDGTIDGGHPQRPASPRLRSPLLRLATWNVNSIRTRLDRVLDWLGRADVDVLAMQETKCPDGQFPALPLFELGYDVAHVGFDQWNGVAIASRVGLDDVRVGFDGQPSWSGKPEVAATTEARALGATCGGIRVWSLYVPNGRALDDPHYTYKLDWLAALRDTAEGWLRDDPAAPIALMGDWNIAPTDDDVWSTEFFAGCTHVSEPERKAFNAIVDAQFTDVVRPFTPGPGVYTYWDYTQLRFPKKQGMRIDFILGSPALAARVMDAQIVREERKGKAPSDHAPVLVDLHAG","organism":"Mycobacterium tuberculosis","uniprot_code":"A0A0T9L251","uniprot_range_first":1,"uniprot_range_last":291,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":null,"mw":32.108,"total_mw":32.108,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"50 mM Tris-HCl 500 mM NaCl 5mM β-mercaptoethanol","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":8.0,"deuteration":null},"purity_method":null,"name":"class II apurinic/apyrimidinic-endonuclease/3'-5' exonuclease III","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":null,"address":"India","full_name":"CSIR - Central Drug Research Institute","webpage":"https://cdri.res.in/"}],"contributor_name":"Ravishankar","contributor_surname":"Ramachandran","orcid":""}],"concentration_method":null,"concentration_unit":null,"date":"2017-05-12","storage_temperature":4.0,"cell_temperature":10.0,"exposure_time":1.0,"number_of_frames":10,"wavelength":0.082,"sample_detector_distance":1.1,"concentration_min":null,"concentration_max":5.3,"sample_volume":null,"flow_rate":null,"s_min":0.031,"s_max":4.944,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDDD8_fit1_model1_img.png","software":"DAMMIF","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDDD8_fit1_model1.pdb","model_mw":33.714,"bead_radius":2.0,"log":"https://www.sasbdb.org/media/log_files/tri051sub-2.log","symmetry":"P1","comment":null,"user":328}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDD8_fit1_fixed_fit_img.png","software":"DAMMIF","chi_square_value":1.361,"p_value":0.0,"fit_residual_plot":"SASDDD8_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDDD8_fit1.fir","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/tri051sub-2.log","software_version":null,"description":null}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"5.0","i0_calibration_standard":null,"description":"CAUTION! The SAXS data at very-low angles (s < 0.21 nm-1) have error estimates and intensities that are unrealistic for a single-concentration SAXS profile and are inconsistent with the remaining dataset.","experiment_description":"Synchrotron SAXS data from solutions of the class II apurinic/apyrimidinic-endonuclease/3'-5' exonuclease III in 50 mM Tris-HCl 500 mM NaCl 5mM β-mercaptoethanol, pH 8 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 1.1 m and at a wavelength of λ = 0.082 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 5.30 mg/ml was measured at 10°C. 10 successive 1 second frames were collected. 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":35.65,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":null,"porod_mw_error":null,"pddf_i0":13.54,"pddf_i0_error":null,"guinier_i0":13.63,"guinier_i0_error":0.013,"pddf_rg":2.353,"pddf_rg_error":null,"guinier_rg":2.37,"guinier_rg_error":0.012,"pddf_dmax":7.31,"pddf_dmax_error":null,"porod_volume":56.2,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":22,"guinier_point_last":110,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDDD8_datloglog_img.png","symmetry":null,"last_modified":"2020-08-13T15:34:48.952980+02:00","bragg_peak":[]}