Hendra virus protein P/V/W PNT3 low-K domain

{
  "code": "SASDVD8",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/A",
  "project": {
    "title": "Unraveling the molecular grammar and the structural transitions underlying the fibrillation of a viral fibrillogenic domain.",
    "publication": {
      "title": "Unraveling the molecular grammar and the structural transitions underlying the fibrillation of a viral fibrillogenic domain.",
      "author_list": "Gondelaud F, Leval J, Arora L, Walimbe A, Bignon C, Ptchelkine D, Brocca S, Mukhopadyay S, Longhi S",
      "journal": "Protein Sci",
      "doi": "10.1002/pro.70068",
      "pmid": "39985377",
      "published_date": "2025 Mar"
    },
    "status": "released",
    "submitted_date": "2024-10-14",
    "released_date": "2025-02-24"
  },
  "pddf_data": null,
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVD8.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVD8_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVD8_kratky_img.png",
  "pddf_plot": null,
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVD8_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVD8.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": null,
        "name": "Pilatus3 2M",
        "resolution": 0.172
      },
      "name": "ESRF",
      "city": "Grenoble",
      "country": "France",
      "beamline_name": "BM29",
      "beam_geometry": "point",
      "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": "Protein W (artificial PNT3 variant - low-kappa)",
          "short_name": "PNT3 low K",
          "sequence": "MSYYHHHHHHLESTSLYKKAGFTPTREPPVIPEYYYGSGDKGDLSDSPPRGNVNLDSIEIYTSREEERNQLEYEDKFADSSSEVVIKTTPEDNDSINQKEVVGDPSEQGLKHPFPLGEFPEERDTPEVDKDDS",
          "organism": "Hendra virus (isolate Horse/Autralia/Hendra/1994)",
          "uniprot_code": "P0C1C6",
          "uniprot_range_first": 200,
          "uniprot_range_last": 310,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MDKLDLVNDGLDIIDFIQKNQKEIQKTYGRSSIQQPSTKDRTRAWEDFLQSTSGEHEQAE\r\nGGMPKNDGGTEGRNVEDLSSVTSSDGTIGQRVSNTRAWAEDPDDIQLDPMVTDVVYHDHG\r\nGECTGHGPSSSPERGWSYHMSGTHDGNVRAVPDTKVLPNAPKTTVPEEVREIDLIGLEDK\r\nFASAGLNPAAVPFVPKNQSTPTEEPPVIPEYYYGSGRRGDLSKSPPRGNVNLDSIKIYTS\r\nDDEDENQLEYEDEFAKSSSEVVIDTTPEDNDSINQEEVVGDPSDQGLEHPFPLGKFPEKE\r\nETPDVRRKDSLMQDSCKRGGVPKRLPMLSEEFECSGSDDPIIQELEREGSHPGGSLRLRE\r\nPPQSSGNSRNQPDRQLKTGDAASPGGVQRPGTPMPKSRIMPIKKGAQTRSLNMLGRKTCL\r\nGRRVVQPGMFADYPPTKKARVLLRRMSN",
          "mw": 15.198,
          "total_mw": 15.198,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": "Artificial PNT3 variant with an homogeneous opposite charges distribution (low-kappa). The protein construct used for SAXS contains a non-native polyhistitine tag and additional amino acids (MSYYHHHHHHLESTSLYKKAGF)."
        }
      ],
      "buffer": {
        "name": "20 mM HEPES, 150 mM NaCl",
        "concentration_unit": null,
        "comment": "HBS",
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.2,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Hendra virus protein P/V/W PNT3 low-K domain",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "13288 Marseille, France",
            "full_name": "CNRS, AFMB UMR 7257 ",
            "webpage": ""
          }
        ],
        "contributor_name": "Frank",
        "contributor_surname": "Gondelaud",
        "orcid": ""
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2023-06-13",
    "storage_temperature": 4.0,
    "cell_temperature": 20.0,
    "exposure_time": 1.0,
    "number_of_frames": 600,
    "wavelength": 0.0992,
    "sample_detector_distance": 2.835,
    "concentration_min": null,
    "concentration_max": 5.0,
    "sample_volume": 45.0,
    "flow_rate": 0.3,
    "s_min": 0.091,
    "s_max": 5.253,
    "total_exposure_time": null,
    "seccolumn": 37
  },
  "fits": [
    {
      "models": [],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVD8_fit1_fixed_fit_img.png",
      "software": "EOM/GAJOE",
      "chi_square_value": 1.206,
      "p_value": 0.2299,
      "fit_residual_plot": "SASDVD8_fit1_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVD8_fit1.fit",
      "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/logFile_001_1_MhS9vOT.log",
      "software_version": null,
      "description": "EOM online was used."
    }
  ],
  "estimated_volume_method": null,
  "pddf_software": null,
  "pddf_software_version": null,
  "i0_calibration_standard": null,
  "description": "45 µl were injected on a BioSec 3-300 at a flow rate of 0.3 ml/min in HBS",
  "experiment_description": "Synchrotron SAXS data from solutions of Hendra virus protein P/V/W PNT3 low-K domain in 20 mM HEPES, 150 mM NaCl, pH 7.2 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus3 2M detector at a sample-detector distance of 2.8 m and at a wavelength of λ = 0.0992 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 5 mg/ml was injected at a 0.30 ml/min flow rate onto a Agilent AdvanceBio SEC 2.7 µm - 130 Å column at 20°C. 600 successive 1 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.",
  "tags": [],
  "intensity_unit": "1/cm",
  "experimental_mw": 19.47,
  "experimental_mw_error": null,
  "guinier_i0_mw": null,
  "guinier_i0_mw_error": null,
  "porod_mw": 30.0,
  "porod_mw_error": null,
  "pddf_i0": null,
  "pddf_i0_error": null,
  "guinier_i0": 0.0280077,
  "guinier_i0_error": null,
  "pddf_rg": null,
  "pddf_rg_error": null,
  "guinier_rg": 3.828,
  "guinier_rg_error": 0.192,
  "pddf_dmax": 18.0,
  "pddf_dmax_error": null,
  "porod_volume": 47.6,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 1,
  "guinier_point_last": 43,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDVD8_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2025-02-24T10:52:45.282955+01:00",
  "bragg_peak": []
}

{
  "code": "SASDVD8",
  "status": "success",
  "started_at": "2026-08-11T15:51:19.958438+00:00",
  "finished_at": "2026-08-11T15:51:25.578318+00:00",
  "source_last_modified": "2025-02-24T10:52:45.282955+01:00",
  "files": [
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/rest-api/entry/summary/SASDVD8/",
      "path": "/data/saxsdb/sasbdb/entries/d8/sasdvd8/source/summary.json",
      "size": 7399,
      "sha256": "31d9eb811e1a364d5630b2253f3d95a9593510a00d6c157ece9dccca542d3e95"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/intensities_files/SASDVD8.dat",
      "path": "/data/saxsdb/sasbdb/entries/d8/sasdvd8/source/SASDVD8.dat",
      "size": 47638,
      "sha256": "d4588f17729dffe1b2c2d13d3582a001fbaef43913b3242b021a48435c6f1dc2",
      "role": "curve"
    },
    {
      "role": "pddf",
      "status": "not_listed",
      "path": "/data/saxsdb/sasbdb/entries/d8/sasdvd8/source/SASDVD8.out"
    },
    {
      "status": "not_available",
      "url": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVD8.sascif",
      "path": "/data/saxsdb/sasbdb/entries/d8/sasdvd8/source/SASDVD8.sascif",
      "role": "sascif"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/zip_directories/SASDVD8.zip",
      "path": "/data/saxsdb/sasbdb/entries/d8/sasdvd8/source/SASDVD8.zip",
      "size": 34536,
      "sha256": "ae0297776a3c108f70c916f8c0adaca560631d5bea7645ef5f76a22997c764f3",
      "role": "full_entry_zip",
      "zip_member_count": 3,
      "zip_validation": "central_directory_readable"
    }
  ]
}