Type II toxin-antitoxin system HicB family antitoxin - HicB protein

{
  "code": "SASDD45",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/A",
  "project": {
    "title": "The molecular basis of protein toxin HicA-dependent binding of the protein antitoxin HicB to DNA.",
    "publication": {
      "title": "The molecular basis of protein toxin HicA-dependent binding of the protein antitoxin HicB to DNA.",
      "author_list": "Winter AJ, Williams C, Isupov MN, Crocker H, Gromova M, Marsh P, Wilkinson OJ, Dillingham MS, Harmer NJ, Titball RW, Crump MP",
      "journal": "J Biol Chem",
      "doi": "10.1074/jbc.RA118.005173",
      "pmid": "30337369",
      "published_date": "2018 Oct 18"
    },
    "status": "released",
    "submitted_date": "2018-03-17",
    "released_date": "2018-11-03"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDD45_revised.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDD45.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD45_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD45_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDD45_revised_pofr_img.png",
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  "experiment": {
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      "detector": {
        "type": null,
        "name": "Pilatus 2M",
        "resolution": null
      },
      "name": "Diamond Light Source",
      "city": "Didcot",
      "country": "UK",
      "beamline_name": "B21",
      "beam_geometry": "1 x 5 mm",
      "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": "Type II toxin-antitoxin system HicB family antitoxin",
          "short_name": "HicB",
          "sequence": "MMEFPIAVHKDDGSVYGVTVPDIPGVHSWGETIDDAIKNTREAIVGHVETLIELGEDVEF\r\nTCSTVEELVAKPEYAGAVWALVSVDLSQLDSKPERINVSIPRFVLHKIDAYVASRHETRS\r\nGFLARAALEALNEGKKHHHHHH",
          "organism": "Burkholderia pseudomallei",
          "uniprot_code": "Q63NA5",
          "uniprot_range_first": 1,
          "uniprot_range_last": 134,
          "oligomerization": "tetramer",
          "molecular_type": "protein",
          "uniprot_sequence": "MEFPIAVHKDDGSVYGVTVPDIPGVHSWGETIDDAIKNTREAIVGHVETLIELGEDVEFT\nCSTVEELVAKPEYAGAVWALVSVDLSQLDSKPERINVSIPRFVLHKIDAYVASRHETRSG\nFLARAALEALNEGKVRHA",
          "mw": 15.739,
          "total_mw": 62.956,
          "number_molecules": 4,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "25 mM Tris, 150 mM NaCl",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Type II toxin-antitoxin system HicB family antitoxin - HicB protein",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Bristol, UK",
            "full_name": "University of Bristol",
            "webpage": "http://www.bristol.ac.uk"
          }
        ],
        "contributor_name": "Ash",
        "contributor_surname": "Winter",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2016-07-28",
    "storage_temperature": 4.0,
    "cell_temperature": 25.0,
    "exposure_time": 3.0,
    "number_of_frames": null,
    "wavelength": 0.1,
    "sample_detector_distance": 4.014,
    "concentration_min": null,
    "concentration_max": 5.0,
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    "flow_rate": null,
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    "s_max": 4.075,
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    "seccolumn": null
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          "software": "PyMOL",
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              "ext_code": "6G1N",
              "ext_type": "pdb",
              "difference_with_model": "identical"
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          "comment": null,
          "user": 296
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      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD45_fit1_fitfoxs_img.png",
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      "chi_square_value": 1.975269,
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      "fit_residual_plot": "SASDD45_fit1_fitfoxsresiduals_img.png",
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  "pddf_software_version": "5",
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  "description": "Analysis of the data involved ScÅtter (www.bioisis.net/). The resultant curve was fit with the crystal structure of HicB, PDB Code: 6G1N.",
  "experiment_description": "Synchrotron SAXS data from solutions of HicB protein in 25 mM Tris 150 mM NaCl, pH 7.5, were collected using in-line SEC-SAXS at the B21 beam line at the Diamond Light Source (Oxfordshire, UK) using a Pilatus 2M detector at a sample-detector distance of 4.0 m and at a wavelength of λ = 0.1 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In line SEC-SAXS was performed using an Agilent 1200 HPLC system equipped with a 2.4 mL Superdex S200 column (GE Healthcare). A sample concentration of 5mg/ml was loaded onto the column at a flow rate of 0.04 mL/min. Data frames were collected at 25°C for the entire column elution with an exposure time of 3 seconds per frame through an angular s-range of 0.04-4 nm-1. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted using data frames measured from the flow-through column buffer with no macromolecular sample present.",
  "tags": [],
  "intensity_unit": "arbitrary",
  "experimental_mw": 62.0,
  "experimental_mw_error": null,
  "guinier_i0_mw": null,
  "guinier_i0_mw_error": null,
  "porod_mw": 70.0,
  "porod_mw_error": null,
  "pddf_i0": 0.003825,
  "pddf_i0_error": 5e-05,
  "guinier_i0": 0.00380685,
  "guinier_i0_error": 1e-05,
  "pddf_rg": 3.098,
  "pddf_rg_error": 0.06,
  "guinier_rg": 3.04,
  "guinier_rg_error": 0.056,
  "pddf_dmax": 10.5,
  "pddf_dmax_error": null,
  "porod_volume": 112.0,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 35,
  "guinier_point_last": 121,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDD45_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2020-05-08T08:19:46.838764+02:00",
  "bragg_peak": []
}

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