Urokinase plasminogen activator surface receptor, uPAR, K50C-V70C

{
  "code": "SASDFB2",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/nm",
  "project": {
    "title": "Did evolution create a flexible ligand-binding cavity in the urokinase receptor through deletion of a plesiotypic disulfide bond?",
    "publication": {
      "title": "Did evolution create a flexible ligand-binding cavity in the urokinase receptor through deletion of a plesiotypic disulfide bond?",
      "author_list": "Leth JM, Mertens HDT, Leth-Espensen KZ, Jørgensen TJD, Ploug M",
      "journal": "J Biol Chem",
      "doi": "10.1074/jbc.RA119.007847",
      "pmid": "30894413",
      "published_date": "2019 Mar 20"
    },
    "status": "released",
    "submitted_date": "2019-01-30",
    "released_date": "2019-03-20"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFB2.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFB2.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFB2_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFB2_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFB2_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFB2_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFB2.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": "Urokinase plasminogen activator surface receptor",
          "short_name": "uPAR",
          "sequence": ">sp|Q03405|UPAR_HUMAN Urokinase plasminogen activator surface receptor OS=Homo sapiens GN=PLAUR PE=1 SV=1\nMGHPPLLPLLLLLHTCVPASWGLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEEL\nELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISC\nGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNG\nFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGP\nMNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDV\nQYRSGAAPQPGPAHLSLTITLLMTARLWGGTLLWT\n\n",
          "organism": "Homo sapiens",
          "uniprot_code": "Q03405",
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MGHPPLLPLLLLLHTCVPASWGLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEEL\nELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISC\nGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNG\nFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGP\nMNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDV\nQYRSGAAPQPGPAHLSLTITLLMTARLWGGTLLWT",
          "mw": 36.98,
          "total_mw": 36.98,
          "number_molecules": 1,
          "complex_state": null,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "20 mM PBS, 5 %(v/v) glycerol",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.4,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Urokinase plasminogen activator surface receptor, uPAR, K50C-V70C",
      "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": "Haydyn",
        "contributor_surname": "Mertens",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2017-05-05",
    "storage_temperature": 10.0,
    "cell_temperature": 10.0,
    "exposure_time": 0.05,
    "number_of_frames": 20,
    "wavelength": 0.124,
    "sample_detector_distance": 3.1,
    "concentration_min": 0.3,
    "concentration_max": 2.8,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.086,
    "s_max": 5.035,
    "total_exposure_time": null,
    "seccolumn": null
  },
  "fits": [
    {
      "models": [
        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFB2_fit1_model1_img.png",
          "software": "DAMMIN",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "dummy",
          "software_version": null,
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDFB2_fit1_model1.pdb",
          "model_mw": 34.008,
          "bead_radius": 2.5,
          "log": "https://www.sasbdb.org/media/log_files/ref_IewNu2W.log",
          "symmetry": null,
          "comment": "Refined DAMMIN model from average volume (10 DAMMIF iterations)",
          "user": 12
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/ref_h9zxhiz_fit_img.png",
      "software": "DAMMIN",
      "chi_square_value": 0.982,
      "p_value": 0.135291,
      "fit_residual_plot": "ref_h9zxhiz_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFB2_fit1.fir",
      "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/ref_NTRBGfy.log",
      "software_version": "5.3",
      "description": "Refined DAMMIN model from average volume (10 DAMMIF iterations)"
    }
  ],
  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": "5.0",
  "i0_calibration_standard": null,
  "description": "Introduced disulfide in the first LU domain, DI, of uPAR (K50C-V70C).",
  "experiment_description": "Synchrotron SAXS data from solutions of uPAR K50C-V70C in 20 mM PBS, 5 %(v/v) glycerol, pH 7.4 were collected on the EMBL P12 beam line at PETRA III (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3.1 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.3 and 2.8 mg/ml were measured at 10°C. 20 successive 0.050 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. 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": "1/cm",
  "experimental_mw": 41.18,
  "experimental_mw_error": null,
  "guinier_i0_mw": 41.18,
  "guinier_i0_mw_error": 4.0,
  "porod_mw": 38.9,
  "porod_mw_error": null,
  "pddf_i0": 0.03215,
  "pddf_i0_error": 0.001,
  "guinier_i0": 0.032,
  "guinier_i0_error": 0.001,
  "pddf_rg": 2.661,
  "pddf_rg_error": 0.01,
  "guinier_rg": 2.54,
  "guinier_rg_error": 0.01,
  "pddf_dmax": 9.3,
  "pddf_dmax_error": 0.5,
  "porod_volume": 66.2,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 1,
  "guinier_point_last": 155,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDFB2_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2023-06-21T07:56:39.492710+02:00",
  "bragg_peak": []
}

{
  "code": "SASDFB2",
  "status": "success",
  "started_at": "2026-08-11T13:34:39.480232+00:00",
  "finished_at": "2026-08-11T13:34:49.212947+00:00",
  "source_last_modified": "2023-06-21T07:56:39.492710+02:00",
  "files": [
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/rest-api/entry/summary/SASDFB2/",
      "path": "/data/saxsdb/sasbdb/entries/b2/sasdfb2/source/summary.json",
      "size": 8272,
      "sha256": "61855fc1cb11b6437ea0dc5e83541e1ffb4770254518773df1a1bacf880a88c0"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/intensities_files/SASDFB2.dat",
      "path": "/data/saxsdb/sasbdb/entries/b2/sasdfb2/source/SASDFB2.dat",
      "size": 84593,
      "sha256": "676b4c327ba049b8aee815fb5b23b7cfc7bc406328949c7ed6860f001faecee8",
      "role": "curve"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/p_of_R_files/SASDFB2.out",
      "path": "/data/saxsdb/sasbdb/entries/b2/sasdfb2/source/SASDFB2.out",
      "size": 105196,
      "sha256": "63a24f724c4999f2deac99773a85841515d626b2492bcc6b316d24f71385342f",
      "role": "pddf"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFB2.sascif",
      "path": "/data/saxsdb/sasbdb/entries/b2/sasdfb2/source/SASDFB2.sascif",
      "size": 310365,
      "sha256": "2d3417ea5e76aafea6c68c38621de9873098382fc5afab1be7d220bbe7dfadc8",
      "role": "sascif"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/zip_directories/SASDFB2.zip",
      "path": "/data/saxsdb/sasbdb/entries/b2/sasdfb2/source/SASDFB2.zip",
      "size": 76368,
      "sha256": "2acf1c331e5d618ad2981326624e6bd2903862a74ef271a3364b48acfb315093",
      "role": "full_entry_zip",
      "zip_member_count": 4,
      "zip_validation": "central_directory_readable"
    }
  ]
}