Proliferating cell nuclear antigen - SUMOPCNA - Split Fusion Trimer

{
  "code": "SASDEE6",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/A",
  "project": {
    "title": "Conformational Flexibility of Ubiquitin-Modified and SUMO-Modified PCNA Shown by Full-Ensemble Hybrid Methods.",
    "publication": {
      "title": "Conformational Flexibility of Ubiquitin-Modified and SUMO-Modified PCNA Shown by Full-Ensemble Hybrid Methods.",
      "author_list": "Powers KT, Lavering ED, Washington MT",
      "journal": "J Mol Biol",
      "doi": "10.1016/j.jmb.2018.10.017",
      "pmid": "30381149",
      "published_date": "2018 Dec 7"
    },
    "status": "released",
    "submitted_date": "2018-10-16",
    "released_date": "2019-05-09"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEE6.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEE6.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEE6_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEE6_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEE6_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEE6_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEE6.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": null,
        "name": "Pilatus3 X 1M",
        "resolution": 0.172
      },
      "name": "Advanced Photon Source (APS), Argonne National Laboratory",
      "city": "Lemont, IL",
      "country": "USA",
      "beamline_name": "BioCAT 18ID",
      "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": "Proliferating cell nuclear antigen",
          "short_name": "PCNA",
          "sequence": "MGSSHHHHHHSQDPMSDSEVNQEAKPEVKPEVKPET\r\nHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLD\r\nMEDNDIIEAHREQIGGPGETIKFVADGDIGSGSVIIKPFVDMEHPETSIKLEMDQPVDLT\r\nFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKSGFLQFFLAPKFNDEE\r\nMLEAKFE\r\nEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGVEAFQEYRCDHPVT\r\nLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKLMDIDADFLK\r\nIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMIT",
          "organism": "Saccharomyces cerevisiae",
          "uniprot_code": "P15873",
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "trimer",
          "molecular_type": "protein",
          "uniprot_sequence": "MLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGVEAFQEY\nRCDHPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKLMD\nIDADFLKIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMITKETIKFVADGDIGSGSV\nIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFD\nLKSGFLQFFLAPKFNDEE",
          "mw": 41.798,
          "total_mw": 125.394,
          "number_molecules": 3,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "20 mM Tris, 150 mM NaCl, 5% glycerol, 1 mM TCEP",
        "concentration_unit": null,
        "comment": "22C",
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Proliferating cell nuclear antigen - SUMOPCNA - Split Fusion Trimer",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Iowa, USA",
            "full_name": "University of Iowa Carver College of Medicine",
            "webpage": "https://medicine.uiowa.edu/"
          }
        ],
        "contributor_name": "Kyle",
        "contributor_surname": "Powers",
        "orcid": ""
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2018-08-06",
    "storage_temperature": 22.0,
    "cell_temperature": 22.0,
    "exposure_time": 0.5,
    "number_of_frames": 320,
    "wavelength": 0.1033,
    "sample_detector_distance": 3.5,
    "concentration_min": 0.0,
    "concentration_max": 32.5,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.055,
    "s_max": 3.857,
    "total_exposure_time": null,
    "seccolumn": null
  },
  "fits": [
    {
      "models": [
        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEE6_fit1_model1_img.png",
          "software": "UIOWA_BD",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "dummy",
          "software_version": null,
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEE6_fit1_model1.pdb",
          "model_mw": null,
          "bead_radius": null,
          "log": null,
          "symmetry": null,
          "comment": "One representative PDB from the simulation.",
          "user": 377
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/EnsembleSUMO_fit_img.png",
      "software": "CRYSOL",
      "chi_square_value": 2.581,
      "p_value": 0.0,
      "fit_residual_plot": "EnsembleSUMO_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEE6_fit1.fit",
      "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/nohup_eMzMQqx.out",
      "software_version": "2.7.2",
      "description": "This is a fit derived from 10,000 crysol fit calculations using full simulation ensemble. The log file is reflective of this including all of the individual crysol calculations."
    }
  ],
  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": "5.0",
  "i0_calibration_standard": null,
  "description": null,
  "experiment_description": "Synchrotron SAXS data were collected using size-exclusion chromatography SAXS (SEC-SAXS) on the BioCAT 18-ID beam line at the Advanced Photon Source (APS), Argonne National Laboratory (Lemont, IL, USA). Data were acquired using a reverse-biased silicon diode array Pilatus3 1M detector at a sample-detector distance of 3.5 m and at a wavelength of λ = 0.1033 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Poly-histidine tagged SUMO-proliferating cell nuclear antigen (SUMOPCNA) was measured as a split fusion protein (PCNA (1-163, His-SUMO-165-258) at a sample injection concentration of 32.5 mg/ml at 22°C using a Wyatt Technology WTC-030S5 (SN 0787), WTC - 015 S5 column with a sample injection volume of 500μL sample at a flow-rate of 0.9 mL/min. The mobile phase was 20 mM Tris, 150 mM NaCl, 5% glycerol, 1 mM TCEP, pH 7.5. 320 successive 0.500 second SAXS data frames were collected through the SEC-elution profile that underwent appropriate date reduction, background correction (buffer subtraction) scaling and averaging to generate the profile displayed in this entry. The model represents a one state from an ensemble trajectory of SUMO-modified PCNA. The full ensemble is included in the full-entry zip archive (ca. 300 MB).",
  "tags": [],
  "intensity_unit": "arbitrary",
  "experimental_mw": 125.4,
  "experimental_mw_error": null,
  "guinier_i0_mw": null,
  "guinier_i0_mw_error": null,
  "porod_mw": 194.0,
  "porod_mw_error": null,
  "pddf_i0": 326.4,
  "pddf_i0_error": null,
  "guinier_i0": 324.9,
  "guinier_i0_error": 0.5,
  "pddf_rg": 4.65,
  "pddf_rg_error": null,
  "guinier_rg": 4.653,
  "guinier_rg_error": 0.08,
  "pddf_dmax": 16.92,
  "pddf_dmax_error": null,
  "porod_volume": 310.0,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 7,
  "guinier_point_last": 74,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDEE6_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
  "bragg_peak": []
}

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  "started_at": "2026-08-11T15:07:49.259772+00:00",
  "finished_at": "2026-08-11T15:10:24.351638+00:00",
  "source_last_modified": "2019-12-06T13:07:15.624532+01:00",
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