Immunoglobulin G1 (pH 2, 0.2 M NaCl), SEC-SAXS data

{
  "code": "SASDW54",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/A",
  "project": {
    "title": " <scp>IgG4</scp>\n              and <scp>IgG1</scp>\n              undergo common acid‐induced compaction into an alternatively folded state",
    "publication": {
      "title": " <scp>IgG4</scp>\n              and <scp>IgG1</scp>\n              undergo common acid‐induced compaction into an alternatively folded state",
      "author_list": "Imamura H, Honda S",
      "journal": "FEBS Letters",
      "doi": "10.1002/1873-3468.70031",
      "pmid": null,
      "published_date": "2025 Mar 17"
    },
    "status": "released",
    "submitted_date": "2024-12-19",
    "released_date": "2025-03-17"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDW54.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDW54.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDW54_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDW54_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDW54_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDW54_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDW54.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": null,
        "name": "Pilatus3 2M",
        "resolution": 0.172
      },
      "name": "Photon Factory (PF), High Energy Accelerator Research Organization (KEK)",
      "city": "Tsukuba",
      "country": "Japan",
      "beamline_name": "BL-10C",
      "beam_geometry": null,
      "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": "humanized immunoglobulin G1 monoclonal antibody (trastuzumab)",
          "short_name": "IgG1",
          "sequence": ">Heavy chain 1\r\nEVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRY\r\nADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSS\r\nASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS\r\nGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGG\r\nPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYN\r\nSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREE\r\nMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRW\r\nQQGNVFSCSVMHEALHNHYTQKSLSLSPGK\r\n>Heavy chain 2\r\nEVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRY\r\nADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSS\r\nASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS\r\nGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGG\r\nPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYN\r\nSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREE\r\nMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRW\r\nQQGNVFSCSVMHEALHNHYTQKSLSLSPGK\r\n>Light chain 1\r\nDIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPS\r\nRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRTVAAPSVFIFPP\r\nSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT\r\nLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC\r\n>Light chain 2\r\nDIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPS\r\nRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRTVAAPSVFIFPP\r\nSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT\r\nLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC",
          "organism": "Mouse/human",
          "uniprot_code": null,
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "",
          "mw": 148.0,
          "total_mw": 148.0,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": "DrugBank ID: DB00072\r\nhttps://go.drugbank.com/drugs/DB00072\r\nHeavy chains' C-terminal K residues are deleted for Herceptin (Chugai Pharmaceutical Co., Ltd., Tokyo, Japan), commercially available trastuzumab, according to the information in PMDA (Pharmaceuticals and Medical Devices Agency): Review report regarding the anti-HER2 humanized monoclonal antibody Herceptin® Injection 60 and 150, on Jan. 16th 2008 (https://www.pmda.go.jp/drugs/2007/P200700066/45004500_21300AMY00128_A100_2.pdf)."
        }
      ],
      "buffer": {
        "name": "100 mM glycine-HCl, 200 mM NaCl",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 2.0,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Immunoglobulin G1 (pH 2, 0.2 M NaCl), SEC-SAXS data",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": null,
            "full_name": "Toyama Prefectural University",
            "webpage": null
          }
        ],
        "contributor_name": "Hiroshi",
        "contributor_surname": "Imamura",
        "orcid": "https://orcid.org/0000-0001-8924-747X"
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2023-05-20",
    "storage_temperature": 4.0,
    "cell_temperature": 25.0,
    "exposure_time": 20.0,
    "number_of_frames": 13,
    "wavelength": 0.15,
    "sample_detector_distance": 2.0,
    "concentration_min": null,
    "concentration_max": 10.0,
    "sample_volume": 400.0,
    "flow_rate": 0.2,
    "s_min": 0.044,
    "s_max": 2.731,
    "total_exposure_time": null,
    "seccolumn": 1
  },
  "fits": [],
  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": "5.0",
  "i0_calibration_standard": null,
  "description": "DrugBank ID: DB00072 https://go.drugbank.com/drugs/DB00072. Heavy chains' C-terminal K residues are deleted for Herceptin (Chugai Pharmaceutical Co., Ltd., Tokyo, Japan), commercially available trastuzumab, according to the information in PMDA (Pharmaceuticals and Medical Devices Agency): Review report regarding the anti-HER2 humanized monoclonal antibody Herceptin® Injection 60 and 150, on Jan. 16th 2008 (https://www.pmda.go.jp/drugs/2007/P200700066/45004500_21300AMY00128_A100_2.pdf).",
  "experiment_description": "Synchrotron SAXS data from solutions of Immunoglobulin G in 100 mM glycine-HCl, 200 mM NaCl, pH 2 were collected on the BL-10C beam line at the Photon Factory High Energy Accelerator Research Organization (KEK; Tsukuba, Japan) using a Pilatus3 2M detector at a sample-detector distance of 2 m and at a wavelength of λ = 0.15 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 400.00 μl sample at 10 mg/ml was injected at a 0.20 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 25°C. 13 successive 20 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": 131.0,
  "experimental_mw_error": null,
  "guinier_i0_mw": 131.0,
  "guinier_i0_mw_error": 0.2,
  "porod_mw": 150.0,
  "porod_mw_error": null,
  "pddf_i0": 0.09482,
  "pddf_i0_error": null,
  "guinier_i0": 0.0956356,
  "guinier_i0_error": null,
  "pddf_rg": 4.17,
  "pddf_rg_error": null,
  "guinier_rg": 4.184,
  "guinier_rg_error": 0.169,
  "pddf_dmax": 12.85,
  "pddf_dmax_error": null,
  "porod_volume": 240.0,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 60,
  "guinier_point_last": 231,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDW54_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2025-03-17T16:06:56.010203+01:00",
  "bragg_peak": []
}

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  "finished_at": "2026-08-11T14:14:34.400523+00:00",
  "source_last_modified": "2025-03-17T16:06:56.010203+01:00",
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