{ "code": "SASDFF6", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/nm", "project": { "title": "Regulation of futile ligation during early steps of BER in M. tuberculosis is carried out by a β-clamp-XthA-LigA tri-component complex", "publication": { "title": "Regulation of futile ligation during early steps of BER in M. tuberculosis is carried out by a β-clamp-XthA-LigA tri-component complex", "author_list": "Shukla A, Afsar M, Khanam T, Kumar N, Ali F, Kumar S, Jahan F, Ramachandran R", "journal": "International Journal of Biological Macromolecules", "doi": "10.1016/j.ijbiomac.2022.11.094", "pmid": null, "published_date": "2022 Nov" }, "status": "released", "submitted_date": "2019-05-24", "released_date": "2021-09-27" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFF6.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFF6.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFF6_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFF6_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFF6_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFF6_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFF6.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": "Beta sliding clamp", "short_name": null, "sequence": "MDAATTRVGLTDLTFRLLRESFADAVSWVAKNLPARPAVPVLSGVLLTGSDNGLTISGFDYEVSAEAQVGAEIVSPGSVLVSGRLLSDITRALPNKPVDVHVEGNRVALTCGNARFSLPTMPVEDYPTLPTLPEETGLLPAELFAEAISQVAIAAGRDDTLPMLTGIRVEILGETVVLAATDRFRLAVRELKWSASSPDIEAAVLVPAKTLAEAAKAGIGGSDVRLSLGTGPGVGKDGLLGISGNGKRSTTRLLDAEFPKFRQLLPTEHTAVATMDVAELIEAIKLVALVADRGAQVRMEFADGSVRLSAGADDVGRAEEDLVVDYAGEPLTIAFNPTYLTDGLSSLRSERVSFGFTTAGKPALLRPVSGDDRPVAGLNGNGPFPAVSTDYVYLLMPVRLPGHHHHHH", "organism": "Mycobacterium tuberculosis", "uniprot_code": "P9WNU1", "uniprot_range_first": 1, "uniprot_range_last": 402, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MDAATTRVGLTDLTFRLLRESFADAVSWVAKNLPARPAVPVLSGVLLTGSDNGLTISGFD\nYEVSAEAQVGAEIVSPGSVLVSGRLLSDITRALPNKPVDVHVEGNRVALTCGNARFSLPT\nMPVEDYPTLPTLPEETGLLPAELFAEAISQVAIAAGRDDTLPMLTGIRVEILGETVVLAA\nTDRFRLAVRELKWSASSPDIEAAVLVPAKTLAEAAKAGIGGSDVRLSLGTGPGVGKDGLL\nGISGNGKRSTTRLLDAEFPKFRQLLPTEHTAVATMDVAELIEAIKLVALVADRGAQVRME\nFADGSVRLSAGADDVGRAEEDLVVDYAGEPLTIAFNPTYLTDGLSSLRSERVSFGFTTAG\nKPALLRPVSGDDRPVAGLNGNGPFPAVSTDYVYLLMPVRLPG", "mw": 42.935, "total_mw": 85.87, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "Probable exodeoxyribonuclease III protein XthA (Exonuclease III) (EXO III) (AP endonuclease VI)", "short_name": null, "sequence": "MPDGTIDGGHPQRPASPRLRSPLLRLATWNVNSIRTRLDRVLDWLGRADV DVLAMQETKCPDGQFPALPLFELGYDVAHVGFDQWNGVAIASRVGLDDVR VGFDGQPSWSGKPEVAATTEARALGATCGGIRVWSLYVPNGRALDDPHYT YKLDWLAALRDTAEGWLRDDPAAPIALMGDWNIAPTDDDVWSTEFFAGCT HVSEPERKAFNAIVDAQFTDVVRPFTPGPGVYTYWDYTQLRFPKKQGMRI DFILGSPALAARVMDAQIVREERKGKAPSDHAPVLVDLHAGHHHHHH", "organism": "Mycobacterium tuberculosis", "uniprot_code": "P96273", "uniprot_range_first": 1, "uniprot_range_last": 291, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MPDGTIDGGHPQRPASPRLRSPLLRLATWNVNSIRTRLDRVLDWLGRADVDVLAMQETKC\nPDGQFPALPLFELGYDVAHVGFDQWNGVAIASRVGLDDVRVGFDGQPSWSGKPEVAATTE\nARALGATCGGIRVWSLYVPNGRALDDPHYTYKLDWLAALRDTAEGWLRDDPAAPIALMGD\nWNIAPTDDDVWSTEFFAGCTHVSEPERKAFNAIVDAQFTDVVRPFTPGPGVYTYWDYTQL\nRFPKKQGMRIDFILGSPALAARVMDAQIVREERKGKAPSDHAPVLVDLHAG", "mw": 32.931, "total_mw": 32.931, "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": "Probable exodeoxyribonuclease III protein XthA, sliding beta clamp complex", "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": "2017-05-15", "storage_temperature": 4.0, "cell_temperature": 10.0, "exposure_time": 1.0, "number_of_frames": 10, "wavelength": 0.0992, "sample_detector_distance": 2.867, "concentration_min": null, "concentration_max": 2.5, "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/SASDFF6_fit1_model1_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "DAMAVER", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDFF6_fit1_model1.pdb", "model_mw": 26.56, "bead_radius": 3.0, "log": "https://www.sasbdb.org/media/log_files/complex_412_sub-XthA_Beta_rnTlATt.log", "symmetry": null, "comment": null, "user": 328 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDFF6_fit1_fixed_fit_img.png", "software": "DAMMIF", "chi_square_value": 0.774, "p_value": 0.340933, "fit_residual_plot": "SASDFF6_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFF6_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/complex_412_sub-XthA_Beta.log", "software_version": null, "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": "The presented model shows the spatial alignment of several individually calculated models and does not fit the SAXS data. A corresponding individual model fit (individual model not provided for this entry) is shown.", "experiment_description": "Synchrotron SAXS data from solutions of probable exodeoxyribonuclease III protein XthA bound to sliding beta clamp in 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH 8 were collected on the BM29 beam line at the ESRF storage ring (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.0992 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 2.50 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": 125.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 61.0, "porod_mw_error": null, "pddf_i0": 12.85, "pddf_i0_error": null, "guinier_i0": 12.98, "guinier_i0_error": 0.058, "pddf_rg": 3.482, "pddf_rg_error": null, "guinier_rg": 3.48, "guinier_rg_error": 0.02, "pddf_dmax": 11.3, "pddf_dmax_error": null, "porod_volume": 98.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 32, "guinier_point_last": 72, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDFF6_datloglog_img.png", "symmetry": null, "last_modified": "2022-11-17T09:57:12.325311+01:00", "bragg_peak": [] }