Glycosylated myelin-associated glycoprotein full extracellular domain (Ig1-5) I473E mutant

{
  "code": "SASDB26",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Structural basis of myelin-associated glycoprotein adhesion and signalling.",
    "publication": {
      "title": "Structural basis of myelin-associated glycoprotein adhesion and signalling.",
      "author_list": "Pronker MF, Lemstra S, Snijder J, Heck AJ, Thies-Weesie DM, Pasterkamp RJ, Janssen BJ",
      "journal": "Nat Commun",
      "doi": "10.1038/ncomms13584",
      "pmid": "27922006",
      "published_date": "2016 Dec 6"
    },
    "status": "released",
    "submitted_date": "2016-07-24",
    "released_date": "2016-12-13"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDB26.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDB26.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB26_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB26_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDB26_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB26_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDB26.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": "Dectris",
        "name": "Pilatus 1M",
        "resolution": 172.0
      },
      "name": "ESRF",
      "city": "Grenoble",
      "country": "France",
      "beamline_name": "BM29",
      "beam_geometry": "",
      "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": "Myelin-associated glycoprotein (20-508; I473E mutant)",
          "short_name": "MAG",
          "sequence": "GHWGAWMPSTISAFEGTCVSIPCRFDFPDELRPAVVHGVWY\r\nFNSPYPKNYPPVVFKSRTQVVHESFQGRSRLLGDLGLRNCTLLLSTLSPELGGKYYFRGD\r\nLGGYNQYTFSEHSVLDIVNTPNIVVPPEVVAGTEVEVSCMVPDNCPELRPELSWLGHEGL\r\nGEPTVLGRLREDEGTWVQVSLLHFVPTREANGHRLGCQAAFPNTTLQFEGYASLDVKYPP\r\nVIVEMNSSVEAIEGSHVSLLCGADSNPPPLLTWMRDGMVLREAVAKSLYLDLEEVTPGED\r\nGVYACLAENAYGQDNRTVELSVMYAPWKPTVNGTVVAVEGETVSILCSTQSNPDPILTIF\r\nKEKQILATVIYESQLQLELPAVTPEDDGEYWCVAENQYGQRATAFNLSVEFAPIILLESH\r\nCAAARDTVQCLCVVKSNPEPSVAFELPSRNVTVNETEREFVYSERSGLLLTSE\r\nLTIRGQA\r\nQAPPRVICTSRNLYGTQSLELPFQGAHR",
          "organism": "Mus musculus",
          "uniprot_code": "P20917",
          "uniprot_range_first": 20,
          "uniprot_range_last": 508,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MIFLATLPLFWIMISASRGGHWGAWMPSTISAFEGTCVSIPCRFDFPDELRPAVVHGVWY\nFNSPYPKNYPPVVFKSRTQVVHESFQGRSRLLGDLGLRNCTLLLSTLSPELGGKYYFRGD\nLGGYNQYTFSEHSVLDIVNTPNIVVPPEVVAGTEVEVSCMVPDNCPELRPELSWLGHEGL\nGEPTVLGRLREDEGTWVQVSLLHFVPTREANGHRLGCQAAFPNTTLQFEGYASLDVKYPP\nVIVEMNSSVEAIEGSHVSLLCGADSNPPPLLTWMRDGMVLREAVAKSLYLDLEEVTPGED\nGVYACLAENAYGQDNRTVELSVMYAPWKPTVNGTVVAVEGETVSILCSTQSNPDPILTIF\nKEKQILATVIYESQLQLELPAVTPEDDGEYWCVAENQYGQRATAFNLSVEFAPIILLESH\nCAAARDTVQCLCVVKSNPEPSVAFELPSRNVTVNETEREFVYSERSGLLLTSILTIRGQA\nQAPPRVICTSRNLYGTQSLELPFQGAHRLMWAKIGPVGAVVAFAILIAIVCYITQTRRKK\nNVTESSSFSGGDNPHVLYSPEFRISGAPDKYESEKQRLGSERRLLGLRGESPELDLSYSH\nSDLGKRPTKDSYTLTEELAEYAEIRVK",
          "mw": 53.979,
          "total_mw": 53.979,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "20 mM HEPES 150 mM NaCl",
        "concentration_unit": "mM",
        "comment": null,
        "additive": "150 mM NaCl",
        "concentration": 20.0,
        "pka": null,
        "ph": 7.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Glycosylated myelin-associated glycoprotein full extracellular domain (Ig1-5) I473E mutant",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Utrecht, Netherlands",
            "full_name": "Utrecht University",
            "webpage": "http://www.uu.nl/"
          }
        ],
        "contributor_name": "Matti",
        "contributor_surname": "Pronker",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2014-09-11",
    "storage_temperature": 20.0,
    "cell_temperature": 20.0,
    "exposure_time": 2.0,
    "number_of_frames": 9,
    "wavelength": 0.0992,
    "sample_detector_distance": 2.87,
    "concentration_min": null,
    "concentration_max": 3.0,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.036,
    "s_max": 4.969,
    "total_exposure_time": null,
    "seccolumn": null
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    {
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        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDB26_fit1_model1_img.png",
          "software": "PDB (Protein Data Bank)",
          "pdb_link": [
            {
              "pdb_code": "5lfu",
              "ext_code": "5LFU",
              "ext_type": "pdb",
              "difference_with_model": "identical"
            }
          ],
          "model_title": null,
          "type_of_model": "atomic",
          "software_version": "2.8.3",
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDB26_fit1_model1.pdb",
          "model_mw": 56.06,
          "bead_radius": 1.9,
          "log": null,
          "symmetry": "",
          "comment": "",
          "user": 52
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDB26_fit1_fit_img.png",
      "software": null,
      "chi_square_value": 8.708,
      "p_value": 0.0,
      "fit_residual_plot": null,
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDB26_fit1.fit",
      "fit_log": null,
      "software_version": null,
      "description": null
    }
  ],
  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": "Gnom 4.5a",
  "i0_calibration_standard": null,
  "description": "Myelin-associated glycoprotein (MAG) full extracellular domain (immunoglobulin domains 1-5) with an I473E mutation should, based on the crystal structure, convert MAG dimers into monomers.",
  "experiment_description": "Synchrotron SAXS data from solutions of glycosylated myelin-associated glycoprotein (full extracellular domain (Ig1-5) I473E mutant) in HEPES, pH 7.5 were collected on the BM29 camera on the storage ring ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4π sin θ/λ and 2θ is the scattering angle). One solute concentration of 3.00 mg/ml was measured at 20°C. Nine successive 2 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 and the different curves were scaled for protein concentration.",
  "tags": [],
  "intensity_unit": null,
  "experimental_mw": 64.9,
  "experimental_mw_error": null,
  "guinier_i0_mw": 64.4,
  "guinier_i0_mw_error": null,
  "porod_mw": 68.31,
  "porod_mw_error": null,
  "pddf_i0": 64.89,
  "pddf_i0_error": null,
  "guinier_i0": 64.32,
  "guinier_i0_error": null,
  "pddf_rg": 6.27,
  "pddf_rg_error": null,
  "guinier_rg": 6.0,
  "guinier_rg_error": null,
  "pddf_dmax": 20.6,
  "pddf_dmax_error": null,
  "porod_volume": 117.09,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 13,
  "guinier_point_last": 30,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDB26_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
  "bragg_peak": []
}

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  "finished_at": "2026-08-11T16:31:33.237527+00:00",
  "source_last_modified": "2019-12-06T13:07:15.624532+01:00",
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