Pentraxin-3

{
  "code": "SASDVA6",
  "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/SASDVA6.dat",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVA6.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVA6_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVA6_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVA6_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVA6_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVA6.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",
          "short_name": "PTX3",
          "sequence": "ENSDDYDLMYVNLDNEIDNGLHPTEDPTPCACGQEHSEWDKLFIMLENSQMRERMLLQATDDV LRGELQRLRE ELGRLAESLARPCAPGAPAEARLTSALDELLQATRDAGRRLARMEGAEAQRPEEAGRALA AVLEELRQTRADLHAVQGWAARSWLPAGCETAILFPMRSKKIFGSVHPVRPMRLESFSACIWVKATDVLN KTILFSYGTKRNPYEIQLYLSYQSIVFVVGGEENKLVAEAMVSLGRWTHLCGTWNSEEGLTSLWVNGELA ATTVEMATGHIVPEGGILQIGQEKNGCCVGGGFDETLAFSGRLTGFNIWDSVLSNEEIRETGGAESCHIR GNIVGWGVTEIQPHGGAQYVS",
          "organism": "Homo sapiens",
          "uniprot_code": "P26022",
          "uniprot_range_first": 18,
          "uniprot_range_last": 381,
          "oligomerization": "octamer",
          "molecular_type": "protein",
          "uniprot_sequence": "MHLLAILFCALWSAVLAENSDDYDLMYVNLDNEIDNGLHPTEDPTPCACGQEHSEWDKLF\nIMLENSQMRERMLLQATDDVLRGELQRLREELGRLAESLARPCAPGAPAEARLTSALDEL\nLQATRDAGRRLARMEGAEAQRPEEAGRALAAVLEELRQTRADLHAVQGWAARSWLPAGCE\nTAILFPMRSKKIFGSVHPVRPMRLESFSACIWVKATDVLNKTILFSYGTKRNPYEIQLYL\nSYQSIVFVVGGEENKLVAEAMVSLGRWTHLCGTWNSEEGLTSLWVNGELAATTVEMATGH\nIVPEGGILQIGQEKNGCCVGGGFDETLAFSGRLTGFNIWDSVLSNEEIRETGGAESCHIR\nGNIVGWGVTEIQPHGGAQYVS",
          "mw": 40.121,
          "total_mw": 320.968,
          "number_molecules": 8,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": "PTX3 was expressed in Chinese hamster ovary (CHO) cells and is therefore glycosylated. Signal sequence cleaved (amino acids 1-17 of UniProt P26022). D48 isoform."
        }
      ],
      "buffer": {
        "name": "50 mM Tris-HCl, 150 mM NaCl",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.4,
        "deuteration": null
      },
      "purity_method": null,
      "name": "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": "2018-09-28",
    "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": 6.0,
    "sample_volume": 45.0,
    "flow_rate": 0.08,
    "s_min": 0.035,
    "s_max": 3.696,
    "total_exposure_time": null,
    "seccolumn": 59
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          "software": "AllosMod",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "atomic",
          "software_version": null,
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDVA6_fit1_model1.pdb",
          "model_mw": 339.5,
          "bead_radius": null,
          "log": null,
          "symmetry": null,
          "comment": null,
          "user": 1107
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      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVA6_fit1_fixed_fit_img.png",
      "software": "FoXS",
      "chi_square_value": 39.752855,
      "p_value": 0.0,
      "fit_residual_plot": "SASDVA6_fit1_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVA6_fit1.fit",
      "fit_log": null,
      "software_version": null,
      "description": ""
    }
  ],
  "estimated_volume_method": null,
  "pddf_software": "ScÅtter",
  "pddf_software_version": "IV",
  "i0_calibration_standard": null,
  "description": null,
  "experiment_description": "Synchrotron SAXS data from solutions of Pentraxin-3 in 50 mM Tris-HCl, 150 mM NaCl, 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 6 mg/ml was injected at a 0.075 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": 323.873,
  "experimental_mw_error": null,
  "guinier_i0_mw": null,
  "guinier_i0_mw_error": null,
  "porod_mw": null,
  "porod_mw_error": null,
  "pddf_i0": 53.79153,
  "pddf_i0_error": null,
  "guinier_i0": 0.487172,
  "guinier_i0_error": null,
  "pddf_rg": 9.73,
  "pddf_rg_error": null,
  "guinier_rg": 8.649,
  "guinier_rg_error": 0.397,
  "pddf_dmax": 43.05,
  "pddf_dmax_error": null,
  "porod_volume": 658.0,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 10,
  "guinier_point_last": 49,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDVA6_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2025-07-27T15:24:01.838202+02:00",
  "bragg_peak": []
}

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  "finished_at": "2026-08-11T15:05:30.223846+00:00",
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