4-hydroxy-tetrahydrodipicolinate synthase (DHDPS-apo) from C. botulinum

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  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/A",
  "project": {
    "title": "Substrate Locking Promotes Dimer-Dimer Docking of an Enzyme Antibiotic Target.",
    "publication": {
      "title": "Substrate Locking Promotes Dimer-Dimer Docking of an Enzyme Antibiotic Target.",
      "author_list": "Atkinson SC, Dogovski C, Wood K, Griffin MDW, Gorman MA, Hor L, Reboul CF, Buckle AM, Wuttke J, Parker MW, Dobson RCJ, Perugini MA",
      "journal": "Structure",
      "doi": "10.1016/j.str.2018.04.014",
      "pmid": "29804823",
      "published_date": "2018 Jul 3"
    },
    "status": "released",
    "submitted_date": "2018-04-09",
    "released_date": "2018-05-29"
  },
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  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDV5_pofr_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,
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      "line_collimation_integrationwidth": null,
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      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
        {
          "long_name": "4-hydroxy-tetrahydrodipicolinate synthase from Clostridium botulinum",
          "short_name": "Cbot-DHDPS",
          "sequence": "SIFKGSGVAIITPFTNTGVDFDKLSELIEWHIKSKTDAIIVCGTTGEATTMTETERKET\r\nIKFVIDKVNKRIPVIAGTGSNNTAASIAMSKWAESIGVDGLLVITPYYNKTTQKGLVKHF\r\nKAVSDAVSTPIIIYNVPGRTGLNITPGTLKELCEDKNIVAVKEASGNISQIAQIKALCGD\r\nKLDIYSGNDDQIIPILALGGIGVISVLANVIPEDVHNMCELYLNGKVNEALKIQLDSLAL\r\nTNALFIETNPIPVKTAMNLMNMKVGDLRLPLCEMNENNLEILKKELKAYNLM",
          "organism": "Clostridium botulinum",
          "uniprot_code": "A5I6N2",
          "uniprot_range_first": 2,
          "uniprot_range_last": 292,
          "oligomerization": "tetramer",
          "molecular_type": "protein",
          "uniprot_sequence": "MSIFKGSGVAIITPFTNTGVDFDKLSELIEWHIKSKTDAIIVCGTTGEATTMTETERKET\nIKFVIDKVNKRIPVIAGTGSNNTAASIAMSKWAESIGVDGLLVITPYYNKTTQKGLVKHF\nKAVSDAVSTPIIIYNVPGRTGLNITPGTLKELCEDKNIVAVKEASGNISQIAQIKALCGD\nKLDIYSGNDDQIIPILALGGIGVISVLANVIPEDVHNMCELYLNGKVNEALKIQLDSLAL\nTNALFIETNPIPVKTAMNLMNMKVGDLRLPLCEMNENNLEILKKELKAYNLM",
          "mw": 31.519,
          "total_mw": 126.076,
          "number_molecules": 4,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "20mM Tris, 150mM 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 (DHDPS-apo) from C. botulinum",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Melbourne, Australia",
            "full_name": "Monash University",
            "webpage": "http://www.monash.edu/"
          }
        ],
        "contributor_name": "Sarah",
        "contributor_surname": "Atkinson",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2010-11-26",
    "storage_temperature": 4.0,
    "cell_temperature": 25.0,
    "exposure_time": 5.0,
    "number_of_frames": 7,
    "wavelength": 0.10332,
    "sample_detector_distance": 0.9,
    "concentration_min": null,
    "concentration_max": 9.5,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.23,
    "s_max": 3.598,
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  "fits": [],
  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": "4.5a",
  "i0_calibration_standard": null,
  "description": null,
  "experiment_description": "Synchrotron SAXS data from solutions of 4-hydroxy-tetrahydrodipicolinate synthase (DHDPS-apo) from C. botulinum in 20mM Tris, 150mM NaCl, pH 8, were collected on the SAXS/WAXS beam line at the Australian Synchrotron (Melbourne, Australia) using a Pilatus 1M detector at a sample-detector distance of 0.9 m and at a wavelength of λ = 0.10332 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). The protein sample analyzed was subjected to in-line size exclusion chromatography on a Superdex 200 5/150 GL gel-filtration column (GE Healthcare) with a bed volume of 3 ml equilibrated with buffer at a flow rate of 0.2 ml.min-1. 50 µL Cbot-DHDPS at 300 µM was injected and the fractionated sample flowed through a 1.5 mm quartz capillary where it was exposed to the X-ray beam at 25°C. Seven successive 5 second frames were collected through the SEC-elution profile. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of an appropriate SEC solvent-blank was subtracted.",
  "tags": [],
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  "guinier_i0_error": 0.000111,
  "pddf_rg": 3.16,
  "pddf_rg_error": null,
  "guinier_rg": 3.22,
  "guinier_rg_error": 0.016,
  "pddf_dmax": 9.0,
  "pddf_dmax_error": null,
  "porod_volume": 159.0,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 1,
  "guinier_point_last": 27,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDDV5_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
  "bragg_peak": []
}

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  "source_last_modified": "2019-12-06T13:07:15.624532+01:00",
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