ABC transporter periplasmic substrate-binding protein TupA measured in the absence of metal ligand (tungstate or molybdate)

{
  "code": "SASDBD9",
  "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"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBD9.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBD9.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBD9_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBD9_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBD9_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBD9_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBD9.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": null,
        "name": "Pilatus 2M",
        "resolution": null
      },
      "name": "PETRA III",
      "city": "DESY; Hamburg",
      "country": "Germany",
      "beamline_name": "EMBL P12",
      "beam_geometry": null,
      "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": "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 absence of metal ligand (tungstate or molybdate)",
      "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": "2013-12-07",
    "storage_temperature": 7.0,
    "cell_temperature": 7.0,
    "exposure_time": 0.045,
    "number_of_frames": 20,
    "wavelength": 0.124,
    "sample_detector_distance": 3.0,
    "concentration_min": 1.0,
    "concentration_max": 6.0,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.03,
    "s_max": 4.443,
    "total_exposure_time": null,
    "seccolumn": null
  },
  "fits": [
    {
      "models": [
        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBD9_fit1_model1_img.png",
          "software": "SREFLEX",
          "pdb_link": [
            {
              "pdb_code": "5my5",
              "ext_code": "5MY5",
              "ext_type": "pdb",
              "difference_with_model": "derived"
            }
          ],
          "model_title": null,
          "type_of_model": "atomic",
          "software_version": "2.8.0",
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          "model_mw": 29.44,
          "bead_radius": 1.9,
          "log": null,
          "symmetry": "",
          "comment": "",
          "user": 145
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBD9_fit1_fit_img.png",
      "software": "CRYSOL",
      "chi_square_value": 1.023,
      "p_value": 0.123,
      "fit_residual_plot": "SASDBD9_fit1_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBD9_fit1.fit",
      "fit_log": null,
      "software_version": "28",
      "description": null
    }
  ],
  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": "GNOM v5.0 r8111",
  "i0_calibration_standard": null,
  "description": "TupA protein measured without ligand, fitted against the apo-form model.",
  "experiment_description": "Synchrotron SAXS data from solutions of TupA measured in the absence of metal ligand (tungstate or molybdate) in 5 mM Tris-HCl, pH 7.6 were collected on the P12 beam line at the PETRA III storage ring (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Solute concentrations ranging between 1 and 6 mg/ml were measured at 7°C. 20 successive 0.045 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": 29.1,
  "experimental_mw_error": null,
  "guinier_i0_mw": 29.1,
  "guinier_i0_mw_error": 2.0,
  "porod_mw": 31.0,
  "porod_mw_error": null,
  "pddf_i0": 871.0,
  "pddf_i0_error": 5.0,
  "guinier_i0": 855.0,
  "guinier_i0_error": 5.0,
  "pddf_rg": 2.55,
  "pddf_rg_error": 0.03,
  "guinier_rg": 2.42,
  "guinier_rg_error": 0.04,
  "pddf_dmax": 9.6,
  "pddf_dmax_error": 0.3,
  "porod_volume": 51.4,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 8,
  "guinier_point_last": 64,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDBD9_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2023-06-21T07:56:39.492710+02:00",
  "bragg_peak": []
}

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