{ "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": [] }