Non Structural Protein 15 in complex with RNA 9mer

{
  "code": "SASDX67",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Non Structural Protein 15 in Complex with RNA 9mer Oligo of  SARS CoV 2",
    "publication": null,
    "status": "released",
    "submitted_date": "2025-07-30",
    "released_date": "2025-08-05"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDX67.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDX67.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX67_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX67_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDX67_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX67_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDX67.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": "Hybrid Photon Counting (HPC)",
        "name": "Mythen2 R 1K",
        "resolution": null
      },
      "name": "CSIR-Central Drug Research Institute",
      "city": "Lucknow",
      "country": "India",
      "beamline_name": "Anton Paar SAXSpace",
      "beam_geometry": null,
      "type_of_source": "X-ray in house",
      "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": "Non structural Protein 15",
          "short_name": "NSP15",
          "sequence": "MTIFAPQHKADFGIIDGHFNNFANNAQILAFNDFHKIIQQQINNAANTFAATGLCIGDKIVFHGAIHRNEILKFKRAFFKTFGQTNQQMQTTLAMAKITIHDMFKGIAFQFITFDKFIHGQFQKINFHLATRFKFLQITALGKIGFRQLLNNAIDFFVIVELGFNCFTNQGNTIQARLFRTNARLQTFNATFGNQNTITCITKQVNLTIHTAIKKNGQRCTNGFGRFFCNIGHATNTNGANMCRCITFIIPDNGIGCNINTQIIQNFHFRNRFDITFCPQFKRNINRQCGFILKQFNINTIHFGIHGIVNNANRNFTLLTIKMAFVHNIKGNIFQAGSMRP",
          "organism": "Severe acute respiratory syndrome coronavirus 2",
          "uniprot_code": "P0DTD1",
          "uniprot_range_first": 6465,
          "uniprot_range_last": 6798,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": 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          "mw": 233.3,
          "total_mw": 250.74,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": "The sample comprises a hexameric assembly of NSP15 protein (monomer MW ≈ 38.88 kDa) with an estimated hexameric molecular weight of ~233.30 kDa. Each protein hexamer is complexed with six copies of a 9-nucleotide single-stranded RNA (sequence: AAACGACAU), contributing an additional ~17.45 kDa, yielding a total molecular weight of approximately 250.74 kDa. The RNA is presumed to bind symmetrically across the RNA-binding sites of the protein hexamer, maintaining a compact, globular assembly in solution."
        }
      ],
      "buffer": {
        "name": "20mM HEPES, 150mM Nacl",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Non Structural Protein 15 in complex with RNA 9mer",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "India",
            "full_name": "CSIR - Central Drug Research Institute",
            "webpage": "https://cdri.res.in/"
          }
        ],
        "contributor_name": "Hira Singh",
        "contributor_surname": "Gariya",
        "orcid": ""
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2024-06-14",
    "storage_temperature": 10.0,
    "cell_temperature": 10.0,
    "exposure_time": 900.0,
    "number_of_frames": 3,
    "wavelength": 1.54,
    "sample_detector_distance": 0.317,
    "concentration_min": null,
    "concentration_max": 4.0,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.126,
    "s_max": 5.001,
    "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": "Small-angle X-ray scattering (SAXS) measurements were performed to characterize the solution structure of the SARS-CoV-2 Non-Structural Protein 15 (NSP15) in complex with a 9-mer RNA oligonucleotide (AAACGACAU) under catalytically relevant conditions. NSP15 is a uridine-specific endoribonuclease that functions as a hexamer. The SAXS sample was prepared in the presence of Mn²⁺ ions, which are essential for its enzymatic activity and RNA binding. \r\nThe complex was modeled as a single scattering particle composed of six NSP15 monomers, each associated with a 9-mer RNA, and validated through molecular weight estimation from both I(0) and Porod analysis. The SAXS profile supports a monodisperse and compact hexameric assembly of NSP15 in solution. The data correlate well with the known crystallographic structure (e.g., PDB: 7N33), indicating the preservation of the oligomeric state and RNA interactions in solution under physiological ionic and metal conditions.",
  "experiment_description": null,
  "tags": [],
  "intensity_unit": "arbitrary",
  "experimental_mw": 244.1,
  "experimental_mw_error": null,
  "guinier_i0_mw": 208.0,
  "guinier_i0_mw_error": null,
  "porod_mw": 222.0,
  "porod_mw_error": null,
  "pddf_i0": 51800.0,
  "pddf_i0_error": null,
  "guinier_i0": 52508.4,
  "guinier_i0_error": 842.17,
  "pddf_rg": 4.66,
  "pddf_rg_error": 0.417,
  "guinier_rg": 4.72,
  "guinier_rg_error": 0.18,
  "pddf_dmax": 13.83,
  "pddf_dmax_error": null,
  "porod_volume": 356.0,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 9,
  "guinier_point_last": 30,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDX67_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2025-09-17T14:35:36.817367+02:00",
  "bragg_peak": []
}

{
  "code": "SASDX67",
  "status": "success",
  "started_at": "2026-08-11T15:23:17.271806+00:00",
  "finished_at": "2026-08-11T15:23:24.605774+00:00",
  "source_last_modified": "2025-09-17T14:35:36.817367+02:00",
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