{ "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": [] }