ABC transporter periplasmic substrate-binding protein TupA measured in the presence of tungstate

{
  "code": "SASDBG9",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/A",
  "project": {
    "title": "Highly selective tungstate transporter protein TupA from Desulfovibrio alaskensis G20.",
    "publication": {
      "title": "Highly selective tungstate transporter protein TupA from Desulfovibrio alaskensis G20.",
      "author_list": "Otrelo-Cardoso AR, Nair RR, Correia MAS, Cordeiro RSC, Panjkovich A, Svergun DI, Santos-Silva T, Rivas MG",
      "journal": "Sci Rep",
      "doi": "10.1038/s41598-017-06133-y",
      "pmid": "28724964",
      "published_date": "2017 Jul 19"
    },
    "status": "released",
    "submitted_date": "2017-01-12",
    "released_date": "2017-07-21"
  },
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  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBG9_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBG9_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBG9_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBG9_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBG9.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,
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      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
        {
          "long_name": "ABC transporter periplasmic substrate-binding protein",
          "short_name": null,
          "sequence": "MAHHHHHHVDDDDKMLEVLFQGPEAPVLMMATTTSTDNTGLLDDLAPQFT\r\nKDTGIELRWTAVGTGKALKMGENCDVDILLVHAPAAEKAFVDAGFGTART\r\nQLMYNDFVIIGPAADPAGVKGMTVAAALGKIAADNAVFVSRGDNSGTHKM\r\nEKSLWKQIEGPSPEKEAWYVQTGQGMLRTINVAAEKGGYTMTDRGTYIKY\r\nEASMDGNPPLKILVEGDKILFNQYSAIPVNPAHCPKVKKDLADKFVNWMA\r\nSPATQKTIGDFKLMGKALFTPNAE",
          "organism": "Desulfovibrio alaskensis",
          "uniprot_code": "Q316W1",
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MRKLLLVLALVMSLTGVAYAEAPVLMMATTTSTDNTGLLDDLAPQFTKDTGIELRWTAVG\nTGKALKMGENCDVDILLVHAPAAEKAFVDAGFGTARTQLMYNDFVIIGPAADPAGVKGMT\nVAAALGRIAADNAVFVSRGDNSGTHKMEKSLWKQIEGSSPEKEAWYVQTGQGMLRTINVA\nAEKGGYTMTDRGTYIKYEASMDGNPPLKILVEGDKILFNQYSAIPVNPAHCPKVKKDLAD\nKFVNWMASPATQKTIGDFKLMGKALFTPNAE",
          "mw": 29.66,
          "total_mw": 29.66,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "5 mM Tris-HCl",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.6,
        "deuteration": null
      },
      "purity_method": null,
      "name": "ABC transporter periplasmic substrate-binding protein TupA measured in the presence of tungstate",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": "EMBL-Hamburg",
            "address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
            "full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
            "webpage": "http://www.embl-hamburg.de/index.php"
          }
        ],
        "contributor_name": "Alejandro",
        "contributor_surname": "Panjkovich",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2014-06-21",
    "storage_temperature": 4.0,
    "cell_temperature": 4.9,
    "exposure_time": 1.0,
    "number_of_frames": 10,
    "wavelength": 0.099,
    "sample_detector_distance": 2.867,
    "concentration_min": 0.8,
    "concentration_max": 12.0,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.032,
    "s_max": 4.967,
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    {
      "models": [
        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBG9_fit1_model1_img.png",
          "software": "BUNCH",
          "pdb_link": [
            {
              "pdb_code": "5my5",
              "ext_code": "5MY5",
              "ext_type": "pdb",
              "difference_with_model": "derived"
            }
          ],
          "model_title": null,
          "type_of_model": "mix",
          "software_version": "2.7.2",
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDBG9_fit1_model1.pdb",
          "model_mw": 29.69,
          "bead_radius": 1.9,
          "log": null,
          "symmetry": "",
          "comment": "Tungstate group was added manually by homology to related structures",
          "user": 145
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBG9_fit1_fit_img.png",
      "software": "CRYSOL",
      "chi_square_value": 2.2,
      "p_value": 0.0,
      "fit_residual_plot": "SASDBG9_fit1_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBG9_fit1.fit",
      "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/newbound02.log",
      "software_version": "2.8.0",
      "description": null
    }
  ],
  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": "GNOM v5.0 r8111",
  "i0_calibration_standard": null,
  "description": "TupA measured in the presence of tungstate, fitted against the holo-form model.",
  "experiment_description": "Synchrotron SAXS data from solutions of TupA measured in the presence of tungstate in 5 mM Tris-HCl, pH 7.6 were collected on the BM29 beam line at the ESRF storage ring (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.099 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Solute concentrations ranging between 0.8 and 12 mg/ml were measured at 4.9°C. 10 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 and the different curves were scaled for protein concentration. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.",
  "tags": [],
  "intensity_unit": null,
  "experimental_mw": 29.7,
  "experimental_mw_error": null,
  "guinier_i0_mw": 29.0,
  "guinier_i0_mw_error": 2.0,
  "porod_mw": 27.0,
  "porod_mw_error": null,
  "pddf_i0": 29.2,
  "pddf_i0_error": 0.1,
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  "guinier_i0_error": 0.1,
  "pddf_rg": 2.38,
  "pddf_rg_error": 0.02,
  "guinier_rg": 2.28,
  "guinier_rg_error": 0.03,
  "pddf_dmax": 8.9,
  "pddf_dmax_error": 0.3,
  "porod_volume": 44.4,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 29,
  "guinier_point_last": 114,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDBG9_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
  "bragg_peak": []
}

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