Glutamate/aspartate import solute-binding protein (DEBP) in the presence of glutamate - Glu-bound 10-fold excess

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    "title": "Structure-based screening of binding affinities via small-angle X-ray scattering",
    "publication": {
      "title": "Structure-based screening of binding affinities via small-angle X-ray scattering",
      "author_list": "Chen P, Masiewicz P, Perez K, Hennig J",
      "journal": null,
      "doi": "10.1101/715193",
      "pmid": null,
      "published_date": "2019 Jul 31"
    },
    "status": "released",
    "submitted_date": "2019-07-01",
    "released_date": "2019-08-02"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFJ8.out",
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  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFJ8_pofr_img.png",
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  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFJ8.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": "Glutamate/aspartate import solute-binding protein",
          "short_name": null,
          "sequence": "HHHHHHDDAAPAAGSTLDKIAKNGVIVVGHRESSVPFSYYDNQQKVVGYSQDYSNAIVEAVKKKLN\r\nKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNVERQKQAAFSDTIFVVGTRLLTKKG\r\nGDIKDFANLKDKAVVVTSGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAF\r\nMMDDALLAGERAKAKKPDNWEIVGKPQSQEAYGCMLRKDDPQFKKLMDDTIAQVQTSGEA\r\nEKWFDKWFKNPIPPKNLNMNFELSDEMKALFKEPNDKALN",
          "organism": "Escherichia coli",
          "uniprot_code": "P37902",
          "uniprot_range_first": 28,
          "uniprot_range_last": 302,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MQLRKPATAILALALSAGLAQADDAAPAAGSTLDKIAKNGVIVVGHRESSVPFSYYDNQQ\nKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNVER\nQKQAAFSDTIFVVGTRLLTKKGGDIKDFANLKDKAVVVTSGTTSEVLLNKLNEEQKMNMR\nIISAKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWEIVGKPQSQEAYGCMLRK\nDDPQFKKLMDDTIAQVQTSGEAEKWFDKWFKNPIPPKNLNMNFELSDEMKALFKEPNDKA\nLN",
          "mw": 32.052,
          "total_mw": 32.052,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "100 mM NaCl, 20 mM NaPO4, 0.5 mM TCEP",
        "concentration_unit": null,
        "comment": "SEC buffer for PBP experiments",
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.4,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Glutamate/aspartate import solute-binding protein (DEBP) in the presence of glutamate - Glu-bound 10-fold excess",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": "EMBL",
            "address": "Heidelberg, Germany",
            "full_name": "European Molecular Biology Laboratory (EMBL) - Heidelberg",
            "webpage": "https://www.embl.de/"
          }
        ],
        "contributor_name": "Po-chia",
        "contributor_surname": "Chen",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2018-09-10",
    "storage_temperature": null,
    "cell_temperature": 20.0,
    "exposure_time": 2.0,
    "number_of_frames": 12,
    "wavelength": 0.09919,
    "sample_detector_distance": 2.849,
    "concentration_min": null,
    "concentration_max": 2.2,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.031,
    "s_max": 4.946,
    "total_exposure_time": null,
    "seccolumn": null
  },
  "fits": [],
  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": "5.0",
  "i0_calibration_standard": null,
  "description": "Glu-bound DEBP at a ligand:protein ratio of 10:1. Ligand condition is prepared by dissolving glutamate in powder form (Sigma-Aldrich) directly into the SAXS buffer, followed by dilution to the target concentration with additional SAXS buffer.\r\n\r\nNote that the scattering intensity therefore contains Na+ counterions that was not directly subtracted.",
  "experiment_description": "Synchrotron SAXS data from solutions of DEBP with a 10-fold excess of glutamate in 100 mM NaCl, 20 mM NaPO4, 0.5 mM TCEP, pH 7.4 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.8 m and at a wavelength of λ = 0.09919 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 2.20 mg/ml was measured at 20°C. 12 successive 2 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",
  "experimental_mw": 31.0,
  "experimental_mw_error": null,
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  "guinier_i0_mw_error": null,
  "porod_mw": 24.0,
  "porod_mw_error": null,
  "pddf_i0": 66.97,
  "pddf_i0_error": null,
  "guinier_i0": 67.06,
  "guinier_i0_error": 0.08,
  "pddf_rg": 2.061,
  "pddf_rg_error": null,
  "guinier_rg": 2.06,
  "guinier_rg_error": 0.13,
  "pddf_dmax": 6.44,
  "pddf_dmax_error": null,
  "porod_volume": 39.0,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 22,
  "guinier_point_last": 128,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDFJ8_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
  "bragg_peak": []
}

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