4-hydroxy-tetrahydrodipicolinate synthase (N84D mutant)

{
  "code": "SASDG36",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/A",
  "project": {
    "title": "Asparagine-84, a regulatory allosteric site residue, helps maintain the quaternary structure of Campylobacter jejuni dihydrodipicolinate synthase.",
    "publication": {
      "title": "Asparagine-84, a regulatory allosteric site residue, helps maintain the quaternary structure of Campylobacter jejuni dihydrodipicolinate synthase.",
      "author_list": "Majdi Yazdi M, Saran S, Mrozowich T, Lehnert C, Patel TR, Sanders DAR, Palmer DRJ",
      "journal": "J Struct Biol",
      "doi": "10.1016/j.jsb.2019.107409",
      "pmid": "31678256",
      "published_date": "2019 Oct 31"
    },
    "status": "released",
    "submitted_date": "2019-09-29",
    "released_date": "2019-11-17"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDG36.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDG36.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG36_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG36_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDG36_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG36_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDG36.sascif",
  "experiment": {
    "instrument": {
      "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": "4-hydroxy-tetrahydrodipicolinate synthase (N84D mutant)",
          "short_name": "HTPA synthase N84D",
          "sequence": "MDKNIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSDATHEAVGLAKFAKEHGADGILSVAPYYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVKEASGNIDKCVDLLAHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF",
          "organism": "Campylobacter jejuni",
          "uniprot_code": "Q9PPB4",
          "uniprot_range_first": 1,
          "uniprot_range_last": 298,
          "oligomerization": "dimer",
          "molecular_type": "protein",
          "uniprot_sequence": "MDKNIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHR\nTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPYYNKPTQQGLY\nEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVKEASGNIDKCVDLLA\nHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDEL\nYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF",
          "mw": 32.671,
          "total_mw": 65.342,
          "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": "4-hydroxy-tetrahydrodipicolinate synthase (N84D mutant)",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Lethbridge, AB, Canada",
            "full_name": "University of Lethbridge",
            "webpage": "http://www.uleth.ca/"
          }
        ],
        "contributor_name": "Trushar",
        "contributor_surname": "Patel",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2017-08-02",
    "storage_temperature": null,
    "cell_temperature": null,
    "exposure_time": 3.0,
    "number_of_frames": 619,
    "wavelength": 0.1,
    "sample_detector_distance": 4.0,
    "concentration_min": null,
    "concentration_max": 10.0,
    "sample_volume": 50.0,
    "flow_rate": 0.16,
    "s_min": 0.066,
    "s_max": 3.898,
    "total_exposure_time": null,
    "seccolumn": 1
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          "comment": null,
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      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/untitled_2637_2_fixed_fit_img.png",
      "software": "DAMMIF",
      "chi_square_value": 1.424,
      "p_value": 0.005573,
      "fit_residual_plot": "untitled_2637_2_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDG36_fit1.fir",
      "fit_log": null,
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  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": "5.0",
  "i0_calibration_standard": null,
  "description": "The models displayed in this entry represent: Top, the averaged (DAMFILT) model obtained from the spatial alignment of several individual DAMMIF models (volume and bead occupancy corrected) and; Bottom, and individual DAMMIF model representative and corresponding fit. Additional individual DAMMIF models (in P1 symmetry) are provided in the full entry zip archive.",
  "experiment_description": "Synchrotron SAXS data from solutions of N84D mutant 4-hydroxy-tetrahydrodipicolinate synthase in 20 mM Tris-HCl, 150 mM NaCl, pH 8 were collected on the B21 beam line at the Diamond Light Source (Didcot, UK) using a Pilatus 2M detector at a sample-detector distance of 4 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 50.00 μl sample at 10 mg/ml was injected at a 0.16 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column . 619 successive 3 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,
  "porod_mw": 54.0,
  "porod_mw_error": null,
  "pddf_i0": 0.07698,
  "pddf_i0_error": 3e-05,
  "guinier_i0": 0.077,
  "guinier_i0_error": 6e-05,
  "pddf_rg": 3.08,
  "pddf_rg_error": 0.02,
  "guinier_rg": 3.1,
  "guinier_rg_error": 0.04,
  "pddf_dmax": 9.5,
  "pddf_dmax_error": null,
  "porod_volume": 108.0,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 6,
  "guinier_point_last": 153,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDG36_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2021-04-22T13:41:03.378678+02:00",
  "bragg_peak": []
}

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