The complex formed between the class II apurinic/apyrimidinic-endonuclease/3'-5' exonuclease III (XthA) bound to the BRCT domain from Mycobacterium tuberculosis DNA ligase

{
  "code": "SASDDQ8",
  "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/SASDDQ8.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDQ8.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDQ8_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDQ8_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDQ8_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDQ8_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDQ8.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": "MPDGTIDGGHPQRPASPRLRSPLLRLATWNVNSIRTRLDRVLDWLGRADVDVLAMQETKCPDGQFPALPLFELGYDVAHVGFDQWNGVAIASRVGLDDVRVGFDGQPSWSGKPEVAATTEARALGATCGGIRVWSLYVPNGRALDDPHYTYKLDWLAALRDTAEGWLRDDPAAPIALMGDWNIAPTDDDVWSTEFFAGCTHVSEPERKAFNAIVDAQFTDVVRPFTPGPGVYTYWDYTQLRFPKKQGMRIDFILGSPALAARVMDAQIVREERKGKAPSDHAPVLVDLHAGHHHHHH",
          "organism": "Mycobacterium tuberculosis",
          "uniprot_code": "A0A0T9L251",
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": null,
          "mw": 32.931,
          "total_mw": 32.931,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        },
        {
          "long_name": "M. tb. LigA BRCT domain",
          "short_name": "BRCT domain",
          "sequence": "VDERDESVPRTLAGLTIVVTGSLTGFSRDDAKEAIVARGGKAAGSVSKKTNYVVAGDSPGSKYDKAVELGVPILDEDGFRRLLADGPASRTHHHHHH",
          "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": 10.272,
          "total_mw": 15.34,
          "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 complex formed between the class II apurinic/apyrimidinic-endonuclease/3'-5' exonuclease III (XthA) bound to 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": "2018-03-09",
    "storage_temperature": 10.0,
    "cell_temperature": 10.0,
    "exposure_time": 1.0,
    "number_of_frames": 10,
    "wavelength": 0.081,
    "sample_detector_distance": 1.1,
    "concentration_min": null,
    "concentration_max": 4.6,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.031,
    "s_max": 4.928,
    "total_exposure_time": null,
    "seccolumn": null
  },
  "fits": [
    {
      "models": [
        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDQ8_fit1_model1_img.png",
          "software": "DAMFILT",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "dummy",
          "software_version": null,
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDDQ8_fit1_model1.pdb",
          "model_mw": 82.686,
          "bead_radius": 3.75,
          "log": null,
          "symmetry": null,
          "comment": null,
          "user": 328
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDQ8_fit1_fixed_fit_img.png",
      "software": "DAMMIF",
      "chi_square_value": 1.301,
      "p_value": 0.0,
      "fit_residual_plot": "SASDDQ8_fit1_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDQ8_fit1.fir",
      "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/RR_169_sub-7.log",
      "software_version": null,
      "description": null
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  ],
  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": "5.0",
  "i0_calibration_standard": null,
  "description": "The ab initio model displayed in this entry represents the spatially aligned, volume and bead-occupancy-corrected (averaged) representation of the protein (DAMFILT). The displayed fit corresponds to an individual model fit to the SAXS data.",
  "experiment_description": "Synchrotron SAXS data from solutions of the complex formed between exodeoxyribonuclease III (XthA) and the BRCT domain from Mycobacterium tuberculosis DNA ligase 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 = 0.081 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 4.60 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",
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  "experimental_mw_error": null,
  "guinier_i0_mw": null,
  "guinier_i0_mw_error": null,
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  "porod_mw_error": null,
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  "pddf_i0_error": 0.2,
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  "guinier_i0_error": 0.1,
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  "pddf_rg_error": 0.03,
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  "guinier_rg_error": 0.01,
  "pddf_dmax": 18.48,
  "pddf_dmax_error": null,
  "porod_volume": 112.0,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 8,
  "guinier_point_last": 69,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDDQ8_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2020-08-13T15:35:09.135521+02:00",
  "bragg_peak": []
}

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