Staphylococcus aureus glucosamine-6-phosphate deaminase

{
  "code": "SASDEB6",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/A",
  "project": {
    "title": "Functional and solution structure studies of amino sugar deacetylase and deaminase enzymes from Staphylococcus aureus.",
    "publication": {
      "title": "Functional and solution structure studies of amino sugar deacetylase and deaminase enzymes from Staphylococcus aureus.",
      "author_list": "Davies JS, Coombes D, Horne CR, Pearce FG, Friemann R, North RA, Dobson RCJ",
      "journal": "FEBS Lett",
      "doi": "10.1002/1873-3468.13289",
      "pmid": "30411345",
      "published_date": "2018 Nov 9"
    },
    "status": "released",
    "submitted_date": "2018-10-09",
    "released_date": "2018-11-13"
  },
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  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEB6_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEB6_guinier_img.png",
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  "experiment": {
    "instrument": {
      "detector": {
        "type": "Dectris",
        "name": "Pilatus 1M",
        "resolution": 172.0
      },
      "name": "Australian  Synchrotron",
      "city": "Melbourne",
      "country": "Australia",
      "beamline_name": "SAXS/WAXS",
      "beam_geometry": "Point",
      "type_of_source": "X-ray synchrotron",
      "point_source": true,
      "line_collimation": null,
      "sample_path_length": null,
      "line_collimation_slitlength": null,
      "line_collimation_integrationwidth": null,
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      "beam_profile_ah": null,
      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
        {
          "long_name": "Glucosamine-6-phosphate deaminase",
          "short_name": null,
          "sequence": ">sp|A8YZR7|NAGB_STAAT Glucosamine-6-phosphate deaminase OS=Staphylococcus aureus (strain USA300 / TCH1516) OX=451516 GN=nagB PE=3 SV=1\r\nMKVLNLGSKKQASFYVACELYKEMAFNQHCKLGLATGGTMTDLYEQLVKLLNKNQLNVDN\r\nVSTFNLDEYVGLTASHPQSYHYYMDDMLFKQYPYFNRKNIHIPNGDADDMNAEASKYNDV\r\nLEQQGQRDIQILGIGENGHIGFNEPGTPFDSVTHIVDLTESTIKANSRYFKNEDDVPKQA\r\nISMGLANILQAKRIILLAFGEKKRAAITHLLNQEISVDVPATLLHKHPNVEIYLDDEACP\r\nKNVAKIHVDEMD",
          "organism": "Staphylococcus aureus",
          "uniprot_code": "A8YZR7",
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "dimer",
          "molecular_type": "protein",
          "uniprot_sequence": "MKVLNLGSKKQASFYVACELYKEMAFNQHCKLGLATGGTMTDLYEQLVKLLNKNQLNVDN\nVSTFNLDEYVGLTASHPQSYHYYMDDMLFKQYPYFNRKNIHIPNGDADDMNAEASKYNDV\nLEQQGQRDIQILGIGENGHIGFNEPGTPFDSVTHIVDLTESTIKANSRYFKNEDDVPKQA\nISMGLANILQAKRIILLAFGEKKRAAITHLLNQEISVDVPATLLHKHPNVEIYLDDEACP\nKNVAKIHVDEMD",
          "mw": 28.467,
          "total_mw": 56.934,
          "number_molecules": 2,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "20 mM Tris-HCl 150 mM NaCl",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 8.0,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Staphylococcus aureus glucosamine-6-phosphate deaminase",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "New Zealand",
            "full_name": "University of Canterbury",
            "webpage": "https://www.canterbury.ac.nz/"
          }
        ],
        "contributor_name": "James",
        "contributor_surname": "Davies",
        "orcid": "https://orcid.org/0000-0003-4029-1650"
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2016-04-26",
    "storage_temperature": 4.0,
    "cell_temperature": 20.0,
    "exposure_time": 1.0,
    "number_of_frames": 999,
    "wavelength": 0.10332,
    "sample_detector_distance": 1.6,
    "concentration_min": null,
    "concentration_max": 6.0,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.121,
    "s_max": 6.866,
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              "difference_with_model": "derived"
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          "comment": "Dimeric structure taken from the E. coli hexameric glucosamine-6-phosphate deaminase.",
          "user": 378
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/nagB_ecoli_Dimer1_fit_img.png",
      "software": "CRYSOL",
      "chi_square_value": 0.536,
      "p_value": 0.0,
      "fit_residual_plot": "nagB_ecoli_Dimer1_fitresiduals_img.png",
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  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": "5.0",
  "i0_calibration_standard": null,
  "description": null,
  "experiment_description": "Synchrotron SAXS data from solutions of Staphylococcus aureus glucosamine-6-phosphate deaminase in 20 mM Tris-HCl, 150 mM NaCl, pH 8 were collected on the SAXS/WAXS beam line at the Australian Synchrotron (Melbourne, Australia) using a Dectris Pilatus 1M detector at a sample-detector distance of 1.6 m and at a wavelength of λ = 0.10332 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 6.00 mg/ml was measured at 20°C. 999 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,
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  "guinier_i0_mw_error": null,
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  "porod_mw_error": null,
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  "guinier_i0_error": 0.0002,
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  "guinier_rg_error": 0.031,
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  "pddf_dmax_error": null,
  "porod_volume": 84.2,
  "porod_volume_error": null,
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  "estimated_volume_error": null,
  "guinier_point_first": 14,
  "guinier_point_last": 47,
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  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDEB6_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
  "bragg_peak": []
}

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