{ "code": "SASDV36", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/nm", "project": { "title": "Open and extended conformation of Human DNA ligase-1", "publication": null, "status": "released", "submitted_date": "2024-08-10", "released_date": "2026-08-10" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDV36.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDV36.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDV36_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDV36_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDV36_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDV36_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDV36.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 1", "short_name": null, "sequence": "MQRSIMSFFHPKKEGKAKKPEKEASNSSRETEPPPKAALKEWNGVVSESDSPVKRPGRKAARVLGSEGEEEDEALSPAKGQKPALDCSQVSPPRPATSPENNASLSDTSPMDSSPSGIPKRRTARKQLPKRTIQEVLEEQSEDEDREAKRKKEEEEEETPKESLTEAEVATEKEGEDGDQPTTPPKPLKTSKAETPTESVSEPEVATKQELQEEEEQTKPPRRAPKTLSSFFTPRKPAVKKEVKEEEPGAPGKEGAAEGPLDPSGYNPAKNNYHPVEDACWKPGQKVPYLAVARTFEKIEEVSARLRMVETLSNLLRSVVALSPPDLLPVLYLSLNHLGPPQQGLELGVGDGVLLKAVAQATGRQLESVRAEAAEKGDVGLVAENSRSTQRLMLPPPPLTASGVFSKFRDIARLTGSASTAKKIDIIKGLFVACRHSEARFIARSLSGRLRLGLAEQSVLAALSQAVSLTPPGQEFPPAMVDAGKGKTAEARKTWLEEQGMILKQTFCEVPDLDRIIPVLLEHGLERLPEHCKLSPGIPLKPMLAHPTRGISEVLKRFEEAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQEDNTGKYPDIISRIPKIKLPSVTSFILDTEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQVQVCLYAFDLIYLNGESLVREPLSRRRQLLRENFVETEGEFVFATSLDTKDIEQIAEFLEQSVKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYLDGVGDTLDLVVIGAYLGRGKRAGRYGGFLLASYDEDSEELQAICKLGTGFSDEELEEHHQSLKALVLPSPRPYVRIDGAVIPDHWLDPSAVWEVKCADLSLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPEQATTSAQVACLYRKQSQIQNQQGEDSGSDPEDTY", "organism": "Homo sapiens", "uniprot_code": "P18858", "uniprot_range_first": 1, "uniprot_range_last": 919, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MQRSIMSFFHPKKEGKAKKPEKEASNSSRETEPPPKAALKEWNGVVSESDSPVKRPGRKA\r\nARVLGSEGEEEDEALSPAKGQKPALDCSQVSPPRPATSPENNASLSDTSPMDSSPSGIPK\r\nRRTARKQLPKRTIQEVLEEQSEDEDREAKRKKEEEEEETPKESLTEAEVATEKEGEDGDQ\r\nPTTPPKPLKTSKAETPTESVSEPEVATKQELQEEEEQTKPPRRAPKTLSSFFTPRKPAVK\r\nKEVKEEEPGAPGKEGAAEGPLDPSGYNPAKNNYHPVEDACWKPGQKVPYLAVARTFEKIE\r\nEVSARLRMVETLSNLLRSVVALSPPDLLPVLYLSLNHLGPPQQGLELGVGDGVLLKAVAQ\r\nATGRQLESVRAEAAEKGDVGLVAENSRSTQRLMLPPPPLTASGVFSKFRDIARLTGSAST\r\nAKKIDIIKGLFVACRHSEARFIARSLSGRLRLGLAEQSVLAALSQAVSLTPPGQEFPPAM\r\nVDAGKGKTAEARKTWLEEQGMILKQTFCEVPDLDRIIPVLLEHGLERLPEHCKLSPGIPL\r\nKPMLAHPTRGISEVLKRFEEAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQEDNTGKYPD\r\nIISRIPKIKLPSVTSFILDTEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQVQVCLYAF\r\nDLIYLNGESLVREPLSRRRQLLRENFVETEGEFVFATSLDTKDIEQIAEFLEQSVKDSCE\r\nGLMVKTLDVDATYEIAKRSHNWLKLKKDYLDGVGDTLDLVVIGAYLGRGKRAGRYGGFLL\r\nASYDEDSEELQAICKLGTGFSDEELEEHHQSLKALVLPSPRPYVRIDGAVIPDHWLDPSA\r\nVWEVKCADLSLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPEQATTSAQVACLYRKQ\r\nSQIQNQQGEDSGSDPEDTY", "mw": 101.735, "total_mw": 101.735, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "" } ], "buffer": { "name": "50 mM HEPES pH 7.5, 200 mM NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": null, "deuteration": null }, "purity_method": null, "name": "Human DNA ligase-1 (apo form)", "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": "farheen", "contributor_surname": "jahan", "orcid": "" } ], "concentration_method": null, "concentration_unit": null, "date": "2024-07-27", "storage_temperature": 4.0, "cell_temperature": 10.0, "exposure_time": 30.0, "number_of_frames": 2, "wavelength": 0.154, "sample_detector_distance": 0.317, "concentration_min": null, "concentration_max": 2.0, "sample_volume": null, "flow_rate": null, "s_min": 0.081, "s_max": 7.793, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDV36_fit1_model1_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "dammif (r12736)", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDV36_fit1_model1.pdb", "model_mw": 27.9, "bead_radius": 3.9, "log": null, "symmetry": null, "comment": null, "user": 883 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDV36_fit1_fixed_fit_img.png", "software": "DAMMIF", "chi_square_value": 1.056, "p_value": 0.0093, "fit_residual_plot": "SASDV36_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDV36_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/ligasecomplex27july-9_LizqQYq.log", "software_version": "ATSAS-3.0.3-1.Win10.AMD64", "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": "CAUTION!! The Porod volume (~53 nm³) and molecular weight estimates calculated from the SAXS data (22-43 kDa) in addition to the volume (~56 nm³) and molecular weight of the DAM model (~28 kDa) are significantly lower than expected for a protein of 100 kDa.", "experiment_description": "SAXS data from solutions of DNA ligase-1 in 50 mM HEPES pH 7.5, 200 mM NaCl were collected using an Anton Pair SAXSpace instrument at the CSIR-Central Drug Research Institute (Lucknow, India) equipped with a Mythen2 R 1K detector at a sample-detector distance of 0.3 m and at a wavelength of λ = 0.154 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 2.00 mg/ml was measured at 10°C. Two successive 30 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": 100.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 13590.0, "pddf_i0_error": null, "guinier_i0": 12983.1, "guinier_i0_error": null, "pddf_rg": 4.194, "pddf_rg_error": null, "guinier_rg": 3.632, "guinier_rg_error": 0.03, "pddf_dmax": 18.35, "pddf_dmax_error": null, "porod_volume": 53.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 14, "guinier_point_last": 44, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDV36_datloglog_img.png", "symmetry": null, "last_modified": "2026-08-11T15:17:31.585336+02:00", "bragg_peak": [] }