{"code":"SASDD88","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/SASDD88.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDD88.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD88_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD88_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDD88_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD88_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDD88.sascif","experiment":{"instrument":{"detector":{"type":"Hybrid Photon Counting (HPC)","name":"Mythen2 R 1K","resolution":null},"name":"CSIR-Central Drug Research Institute","city":"Lucknow","country":"India","beamline_name":"Anton Paar SAXSpace","beam_geometry":null,"type_of_source":"X-ray in house","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":"M.tb. LigA BRCT domain (DNA ligase A)","short_name":"BRCT","sequence":"VDERDESVPRTLAGLTIVVTGSLTGFSRDDAKEAIVARGGKAAGSVSKKTNYVVAGDSPGSKYDKAVELGVPILDEDGFRRLLADGPASRT","organism":"Mycobacterium tuberculosis","uniprot_code":"P9WNV1","uniprot_range_first":601,"uniprot_range_last":691,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MSSPDADQTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPE\nLRTPDSPTQLVGGAGFATDFEPVDHLERMLSLDNAFTADELAAWAGRIHAEVGDAAHYLC\nELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLE\nVRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGH\nVEGFRPATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVK\nVDEVALQRRLGSTSRAPRWAIAYKYPPEEAQTKLLDIRVNVGRTGRITPFAFMTPVKVAG\nSTVGQATLHNASEIKRKGVLIGDTVVIRKAGDVIPEVLGPVVELRDGSEREFIMPTTCPE\nCGSPLAPEKEGDADIRCPNARGCPGQLRERVFHVASRNGLDIEVLGYEAGVALLQAKVIA\nDEGELFALTERDLLRTDLFRTKAGELSANGKRLLVNLDKAKAAPLWRVLVALSIRHVGPT\nAARALATEFGSLDAIAAASTDQLAAVEGVGPTIAAAVTEWFAVDWHREIVDKWRAAGVRM\nVDERDESVPRTLAGLTIVVTGSLTGFSRDDAKEAIVARGGKAAGSVSKKTNYVVAGDSPG\nSKYDKAVELGVPILDEDGFRRLLADGPASRT","mw":9.449,"total_mw":13.4,"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":"The BRCT domain from Mycobacterium tuberculosis DNA ligase","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":"2018-06-02","storage_temperature":10.0,"cell_temperature":10.0,"exposure_time":1800.0,"number_of_frames":2,"wavelength":0.154,"sample_detector_distance":0.3171,"concentration_min":null,"concentration_max":10.0,"sample_volume":null,"flow_rate":null,"s_min":0.091,"s_max":7.368,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDD88_fit1_model1_img.png","software":"DAMMIN","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDD88_fit1_model1.pdb","model_mw":9.46,"bead_radius":1.3,"log":null,"symmetry":"P1","comment":null,"user":328}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD88_fit1_fixed_fit_img.png","software":"DAMMIN","chi_square_value":1.43,"p_value":0.000494,"fit_residual_plot":"SASDD88_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDD88_fit1.fir","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/BRCT_10mg-7.log","software_version":null,"description":null},{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDD88_fit2_model1_img.png","software":"Phyre2","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDD88_fit2_model1.pdb","model_mw":9.447,"bead_radius":null,"log":null,"symmetry":"P1","comment":null,"user":328}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD88_fit2_fixed_fit_img.png","software":"FoXS","chi_square_value":4.498358,"p_value":0.0,"fit_residual_plot":"SASDD88_fit2_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDD88_fit2.fit","fit_log":null,"software_version":null,"description":null},{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDD88_fit3_model1_img.png","software":"elNémo","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDD88_fit3_model1.pdb","model_mw":9.447,"bead_radius":1.9,"log":null,"symmetry":null,"comment":null,"user":328}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/2_BRCT_10mg_fixed_fit_img.png","software":"FoXS","chi_square_value":2.790025,"p_value":0.0,"fit_residual_plot":"2_BRCT_10mg_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDD88_fit3.fit","fit_log":null,"software_version":null,"description":null}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"5.0","i0_calibration_standard":null,"description":"The experimental molecular weight quoted for this entry was evaluated using calibrated size-exclusion chromatography (GE Healthcare Superdex75 10/30 column). The atomistic models displayed in this entry (ribbon format) are a parent Phyre2 protein homology model (top) and one of ten structures obtained from the parent after elNémo normal mode calculations (bottom). Refer to: Kelley et al. (2015) Nature Protocols 10, 845-858; Suhre & Sanejouand (2004) Nucleic Acids Res. 32(Web Server issue): W610–W614.","experiment_description":"In house laboratory SAXS data from a solution of the BRCT domain from M. tuberculosis DNA ligase in 50 mM Tris-HCl 500 mM NaCl 5mM β-mercaptoethanol, pH 8 were collected using an Anton Paar SAXSpace instrument at the CSIR-Central Drug Research Institute (Lucknow, India) using a Dectris Mythen 2R1K detector at a sample-detector distance of 0.3 m and at a wavelength of λ = 0.154 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 10.00 mg/ml was measured at 10°C. Two successive 1800 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":15.3,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":null,"porod_mw_error":null,"pddf_i0":24290.0,"pddf_i0_error":null,"guinier_i0":25148.2,"guinier_i0_error":58.86,"pddf_rg":1.441,"pddf_rg_error":null,"guinier_rg":1.58,"guinier_rg_error":0.02,"pddf_dmax":3.73,"pddf_dmax_error":null,"porod_volume":22.59,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":1,"guinier_point_last":115,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDD88_datloglog_img.png","symmetry":null,"last_modified":"2021-08-18T17:34:34.477729+02:00","bragg_peak":[]}