{"code":"SASDEC6","status":"Published","type_of_curve":"Single concentration","angular_unit":"1/nm","project":{"title":"Salt bridges at the subdomain interfaces of the adenylation domain and active-site residues of <i>Mycobacterium tuberculosis</i>\n              NAD <sup>+</sup>\n              -dependent DNA ligase A (MtbLigA) are important for the initial steps of nick-sealing activity","publication":{"title":"Salt bridges at the subdomain interfaces of the adenylation domain and active-site residues of <i>Mycobacterium tuberculosis</i>\n              NAD <sup>+</sup>\n              -dependent DNA ligase A (MtbLigA) are important for the initial steps of nick-sealing activity","author_list":"Afsar M, Shukla A, Kumar N, Ramachandran R","journal":"Acta Crystallographica Section D Structural Biology","doi":"10.1107/S2059798321003107","pmid":null,"published_date":"2021 May 14"},"status":"released","submitted_date":"2019-09-05","released_date":"2021-05-18"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDEC6.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDEC6.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEC6_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEC6_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEC6_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEC6_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDEC6.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":"DNA ligase A","short_name":null,"sequence":"VSSPDADQTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVGGAGFATDFEPVDHLERMLSLDNAFTADELAAWAGRIHAEVGDAAHYLCELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLEVRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGFRPATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVKVDEVALQRRLGSTSRAPRWAIAYKYPPEHHHHHH","organism":"Mycobacterium tuberculosis","uniprot_code":"P9WNV1","uniprot_range_first":2,"uniprot_range_last":328,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MSSPDADQTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPE\nLRTPDSPTQLVGGAGFATDFEPVDHLERMLSLDNAFTADELAAWAGRIHAEVGDAAHYLC\nELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLE\nVRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGH\nVEGFRPATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVK\nVDEVALQRRLGSTSRAPRWAIAYKYPPEEAQTKLLDIRVNVGRTGRITPFAFMTPVKVAG\nSTVGQATLHNASEIKRKGVLIGDTVVIRKAGDVIPEVLGPVVELRDGSEREFIMPTTCPE\nCGSPLAPEKEGDADIRCPNARGCPGQLRERVFHVASRNGLDIEVLGYEAGVALLQAKVIA\nDEGELFALTERDLLRTDLFRTKAGELSANGKRLLVNLDKAKAAPLWRVLVALSIRHVGPT\nAARALATEFGSLDAIAAASTDQLAAVEGVGPTIAAAVTEWFAVDWHREIVDKWRAAGVRM\nVDERDESVPRTLAGLTIVVTGSLTGFSRDDAKEAIVARGGKAAGSVSKKTNYVVAGDSPG\nSKYDKAVELGVPILDEDGFRRLLADGPASRT","mw":37.519,"total_mw":37.519,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":8.0,"deuteration":null},"purity_method":null,"name":"Adenylation Domain of DNA ligase A with NAD+","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":"2018-10-06","storage_temperature":4.0,"cell_temperature":10.0,"exposure_time":1800.0,"number_of_frames":3,"wavelength":0.154,"sample_detector_distance":0.3,"concentration_min":null,"concentration_max":10.8,"sample_volume":null,"flow_rate":null,"s_min":0.104,"s_max":6.0,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDEC6_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/SASDEC6_fit1_model1.pdb","model_mw":46.8,"bead_radius":2.2,"log":null,"symmetry":"P1","comment":null,"user":328}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEC6_fit1_fixed_fit_img.png","software":"DAMMIF","chi_square_value":0.328,"p_value":0.001009,"fit_residual_plot":"SASDEC6_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDEC6_fit1.fir","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/R4withNAD_001FramesAveraged_000_Process_Q_Transformation_Process_1-10.log","software_version":null,"description":""},{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDEC6_fit2_model1_img.png","software":"GASBOR","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDEC6_fit2_model1.pdb","model_mw":null,"bead_radius":1.9,"log":"https://www.sasbdb.org/media/log_files/R4withNA_2.log","symmetry":null,"comment":null,"user":328}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEC6_fit2_fixed_fit_img.png","software":"GASBOR","chi_square_value":0.29,"p_value":6.2e-05,"fit_residual_plot":"SASDEC6_fit2_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDEC6_fit2.fir","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/R4withNA_2.log","software_version":null,"description":""}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"5.0","i0_calibration_standard":null,"description":null,"experiment_description":"SAXS data from solutions of the adenylation Domain of DNA ligase A with NAD+, in 50 mM Tris-HCl, 200 mM NaCl, 2mM β-mercaptoethanol, pH 8 were collected on the Anton Paar SAXSpace instrument at the CSIR-Central Drug Research Institute storage ring (Lucknow, India) using a Hybrid Photon Counting (HPC) Mythen2 R 1K 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 10.80 mg/ml was measured at 10°C. Three 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":38.0,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":59.0,"porod_mw_error":null,"pddf_i0":595300.0,"pddf_i0_error":null,"guinier_i0":599573.0,"guinier_i0_error":22300.0,"pddf_rg":2.345,"pddf_rg_error":null,"guinier_rg":2.37,"guinier_rg_error":0.13,"pddf_dmax":6.17,"pddf_dmax_error":null,"porod_volume":94.26,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":26,"guinier_point_last":70,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDEC6_datloglog_img.png","symmetry":null,"last_modified":"2021-05-18T08:48:35.422747+02:00","bragg_peak":[]}