Human DNA ligase-1 (apo form)

{
  "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": []
}

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  "code": "SASDV36",
  "status": "success",
  "started_at": "2026-08-11T15:01:11.220787+00:00",
  "finished_at": "2026-08-11T15:01:18.511235+00:00",
  "source_last_modified": "2026-08-11T15:17:31.585336+02:00",
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