Tetramer of Pentraxin-3

{
  "code": "SASDVC6",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/A",
  "project": {
    "title": "The structural organisation of pentraxin-3 and its interactions with heavy chains of inter-α-inhibitor regulate crosslinking of the hyaluronan matrix",
    "publication": {
      "title": "The structural organisation of pentraxin-3 and its interactions with heavy chains of inter-α-inhibitor regulate crosslinking of the hyaluronan matrix",
      "author_list": "Shah A, Zhang X, Snee M, Lockhart-Cairns M, Levy C, Jowitt T, Birchenough H, Dean L, Collins R, Dodd R, Roberts A, Enghild J, Mantovani A, Fontana J, Baldock C, Inforzato A, Richter R, Day A",
      "journal": "Matrix Biology",
      "doi": "10.1016/j.matbio.2025.01.002",
      "pmid": null,
      "published_date": "2025 Apr"
    },
    "status": "released",
    "submitted_date": "2024-08-19",
    "released_date": "2025-07-27"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDVC6.dat",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVC6.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVC6_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVC6_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVC6_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVC6_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVC6.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": null,
        "name": "Pilatus 2M",
        "resolution": null
      },
      "name": "Diamond Light Source",
      "city": "Didcot",
      "country": "UK",
      "beamline_name": "B21",
      "beam_geometry": "1 x 5 mm",
      "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": "Pentraxin-related protein PTX3 (C317S, C318S)",
          "short_name": "Half-PTX3",
          "sequence": "ENSDDYDLMYVNLDNEIDNGLHPTEDPTPCACGQEHSEWDKLFIMLENSQMRERMLLQATDDVLRGELQR LREELGRLAESLARPCAPGAPAEARLTSALDELLQATRDAGRRLARMEGAEAQRPEEAGRALAAVLEELRQTRADLHAVQGWAARSWLPAGCETAILFPMRSKKIFGSVHPVRPMRLESFSACIWVKATDVLNKTILFSYGTKRNPYEIQLYLSYQSIVFVVGGEENKLVAEAMVSLGRWTHLCGTWNSEEGLTSLWVNGELAATTVEMATGHIVPEGGILQIGQEKNGSSVGGGFDETLAFSGRLTGFNIWDSVLSNEEIRETGGAESCHIRGNIVGWGVTEIQPHGGAQYVS",
          "organism": "Homo sapiens",
          "uniprot_code": "P26022",
          "uniprot_range_first": 18,
          "uniprot_range_last": 381,
          "oligomerization": "tetramer",
          "molecular_type": "protein",
          "uniprot_sequence": "MHLLAILFCALWSAVLAENSDDYDLMYVNLDNEIDNGLHPTEDPTPCACGQEHSEWDKLF\nIMLENSQMRERMLLQATDDVLRGELQRLREELGRLAESLARPCAPGAPAEARLTSALDEL\nLQATRDAGRRLARMEGAEAQRPEEAGRALAAVLEELRQTRADLHAVQGWAARSWLPAGCE\nTAILFPMRSKKIFGSVHPVRPMRLESFSACIWVKATDVLNKTILFSYGTKRNPYEIQLYL\nSYQSIVFVVGGEENKLVAEAMVSLGRWTHLCGTWNSEEGLTSLWVNGELAATTVEMATGH\nIVPEGGILQIGQEKNGCCVGGGFDETLAFSGRLTGFNIWDSVLSNEEIRETGGAESCHIR\nGNIVGWGVTEIQPHGGAQYVS",
          "mw": 40.089,
          "total_mw": 160.356,
          "number_molecules": 4,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": "Half-PTX3 was expressed in human embryonic kidney (HEK) Expi293F cells and is therefore glycosylated.\r\nSignal sequence cleaved (amino acids 1-17 of UniProt P26022). A48 isoform. Amino acids C317 and C318 mutated to serine."
        }
      ],
      "buffer": {
        "name": "137 mM NaCl, 2.7 mM KCl, 10 mM phosphate buffer",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.4,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Tetramer of Pentraxin-3",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Manchester, UK",
            "full_name": "University of Manchester",
            "webpage": "http://www.manchester.ac.uk/"
          }
        ],
        "contributor_name": "Anokhi",
        "contributor_surname": "Shah",
        "orcid": "https://orcid.org/0000-0001-9818-5573"
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2020-02-06",
    "storage_temperature": 4.0,
    "cell_temperature": 20.0,
    "exposure_time": 1.0,
    "number_of_frames": 620,
    "wavelength": 0.095,
    "sample_detector_distance": 2.7,
    "concentration_min": null,
    "concentration_max": 8.5,
    "sample_volume": 45.0,
    "flow_rate": 0.08,
    "s_min": 0.026,
    "s_max": 3.4,
    "total_exposure_time": null,
    "seccolumn": 59
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    {
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        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVC6_fit1_model1_img.png",
          "software": "AllosMod",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "atomic",
          "software_version": null,
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDVC6_fit1_model1.pdb",
          "model_mw": 172.3,
          "bead_radius": null,
          "log": null,
          "symmetry": null,
          "comment": null,
          "user": 1107
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVC6_fit1_fixed_fit_img.png",
      "software": "FoXS",
      "chi_square_value": 37.543753,
      "p_value": 0.0,
      "fit_residual_plot": "SASDVC6_fit1_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVC6_fit1.fit",
      "fit_log": null,
      "software_version": null,
      "description": ""
    }
  ],
  "estimated_volume_method": null,
  "pddf_software": "ScÅtter",
  "pddf_software_version": null,
  "i0_calibration_standard": null,
  "description": null,
  "experiment_description": "Synchrotron SAXS data from solutions of Pentraxin-3 (tetramers) in 137 mM NaCl, 2.7 mM KCl, 10 mM phosphate buffer, pH 7.4 were collected on the B21 beam line at the Diamond Light Source (Didcot, UK) using a Pilatus 2M detector at a sample-detector distance of 2.7 m and at a wavelength of λ = 0.095 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 45.00 μl sample at 8.5 mg/ml was injected at a 0.08 ml/min flow rate onto a Cytiva Superose 6 Increase 3.2/300 column at 20°C. 620 successive 1 second frames were collected throughout the entire SEC elution. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.",
  "tags": [],
  "intensity_unit": "arbitrary",
  "experimental_mw": 181.359,
  "experimental_mw_error": null,
  "guinier_i0_mw": 221.504,
  "guinier_i0_mw_error": null,
  "porod_mw": null,
  "porod_mw_error": null,
  "pddf_i0": 14507.64,
  "pddf_i0_error": null,
  "guinier_i0": 0.242423,
  "guinier_i0_error": null,
  "pddf_rg": 7.94,
  "pddf_rg_error": null,
  "guinier_rg": 7.79,
  "guinier_rg_error": 1.351,
  "pddf_dmax": 26.0,
  "pddf_dmax_error": null,
  "porod_volume": 370.0,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 39,
  "guinier_point_last": 61,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDVC6_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2025-07-27T15:24:02.710000+02:00",
  "bragg_peak": []
}

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  "started_at": "2026-08-11T15:06:39.284847+00:00",
  "finished_at": "2026-08-11T15:06:47.600257+00:00",
  "source_last_modified": "2025-07-27T15:24:02.710000+02:00",
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