Escherichia coli TraE protein: A VirB8 homolog from plasmid pKM101

{
  "code": "SASDB75",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "VirB8 homolog TraE from plasmid pKM101 forms a hexameric ring structure and interacts with the VirB6 homolog TraD.",
    "publication": {
      "title": "VirB8 homolog TraE from plasmid pKM101 forms a hexameric ring structure and interacts with the VirB6 homolog TraD.",
      "author_list": "Casu B, Mary C, Sverzhinsky A, Fouillen A, Nanci A, Baron C",
      "journal": "Proc Natl Acad Sci U S A",
      "doi": "10.1073/pnas.1802501115",
      "pmid": "29784815",
      "published_date": "2018 Jun 5"
    },
    "status": "released",
    "submitted_date": "2016-08-12",
    "released_date": "2018-05-10"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDB75.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDB75.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB75_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB75_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDB75_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB75_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDB75.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": "CCD",
        "name": "Finger Lakes CCD",
        "resolution": 0.0
      },
      "name": "Cornell High Energy Synchrotron Source (CHESS)",
      "city": "Ithaca, NY",
      "country": "USA",
      "beamline_name": "G1",
      "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": "Escherichia coli TraE protein (VirB8 homolog)",
          "short_name": "TraE",
          "sequence": "MGSSHHHHHHENLYFQGGTKANKKTGLTREAIKEFNESRKG\r\nLEVDLMDEVLKSRRTAWMVATGSAVVTVFALSLVGYVVHKYSQPIPAHLLTLNEATHEVQ\r\nQVKLTRDQTSYGDEIDKFWLTQYVIHRESYDFYSVQVDYTAVGLMSTPNVAESYQSKFKG\r\nRNGLDKVLGDSETTRVKINSVILDKPHGVATIRFTTVRRVRSNPVDDQPQRWIAIMGYEY\r\nKSLAMNAEQRYVNPLGFRVTSYRVNPEVN",
          "organism": "Escherichia coli",
          "uniprot_code": "Q46703",
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "hexamer",
          "molecular_type": "protein",
          "uniprot_sequence": "MKANKKTGLTREAIKEFNESRKGLEVDLMDEVLKSRRTAWMVATGSAVVTVFALSLVGYV\nVHKYSQPIPAHLLTLNEATHEVQQVKLTRDQTSYGDEIDKFWLTQYVIHRESYDFYSVQV\nDYTAVALMSTPNVAESYQSKFKGRNGLDKVLGDSETARVKINSVILDKPHGVRTIRFTTV\nRRVRTNPVDDQPQRWIAIMGYEYKSLAMNAEQRYVNPLGFRVTSYRVNPEVN",
          "mw": 28.537,
          "total_mw": 171.221,
          "number_molecules": 6,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "50 mM sodium phosphate 300 mM NaCl 40 mM imidazole 0.15 % octyl glucose neopentyl glycol (OGNG)",
        "concentration_unit": "mM",
        "comment": null,
        "additive": "300 mM NaCl, 40 mM imidazole, 0.15 % octyl glucose neopentyl glycol (OGNG)",
        "concentration": 50.0,
        "pka": null,
        "ph": 7.4,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Escherichia coli TraE protein: A VirB8 homolog from plasmid pKM101",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Montréal, Canada",
            "full_name": "Département de biochimie, Université de Montréal",
            "webpage": "http://www.umontreal.ca/"
          }
        ],
        "contributor_name": "Bastien",
        "contributor_surname": "Casu",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2016-06-02",
    "storage_temperature": null,
    "cell_temperature": 20.0,
    "exposure_time": 2.0,
    "number_of_frames": 70,
    "wavelength": null,
    "sample_detector_distance": null,
    "concentration_min": null,
    "concentration_max": null,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.092,
    "s_max": 2.611,
    "total_exposure_time": null,
    "seccolumn": null
  },
  "fits": [
    {
      "models": [
        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDB75_fit1_model1_img.png",
          "software": "GASBOR",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "dummy",
          "software_version": "",
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDB75_fit1_model1.pdb",
          "model_mw": null,
          "bead_radius": 1.9,
          "log": null,
          "symmetry": "P6",
          "comment": "",
          "user": 144
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDB75_fit1_fit_img.png",
      "software": null,
      "chi_square_value": 1.16,
      "p_value": 0.1,
      "fit_residual_plot": "SASDB75_fit1_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDB75_fit1.fir",
      "fit_log": null,
      "software_version": null,
      "description": null
    }
  ],
  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": null,
  "i0_calibration_standard": null,
  "description": "The MW of the TraE/OGNG complex was additionally confirmed using SEC-MALLS (248kDa).",
  "experiment_description": "X-ray synchrotron radiation scattering data from a solution of E. coli TraE protein in 50 mM sodium phosphate, 300 mM NaCl, 40 mM imidazole, 0.15 % octyl glucose neopentyl glycol (OGNG), pH 7.4 were collected using size-exclusion chromatography (SEC) SAXS on the G1 beam line at the CHESS storage ring (Ithaca, USA) using a CCD Finger Lakes CCD detector (I(s) vs s, where s = 4π sin θ/λ; 2θ is the scattering angle; λ = 0.12 nm). The data were collected as 70 successive 2 second frames through the hexameric TraE protein/OGNG elution peak and were normalized to the intensity of the transmitted beam and radially averaged. The scattering of the solvent-blank was subtracted to produce the scattering profile displayed in this entry.",
  "tags": [],
  "intensity_unit": null,
  "experimental_mw": 264.2,
  "experimental_mw_error": null,
  "guinier_i0_mw": null,
  "guinier_i0_mw_error": null,
  "porod_mw": 223.0,
  "porod_mw_error": null,
  "pddf_i0": 0.0094,
  "pddf_i0_error": 3e-05,
  "guinier_i0": 0.0094,
  "guinier_i0_error": 6e-05,
  "pddf_rg": 4.44,
  "pddf_rg_error": 0.013,
  "guinier_rg": 4.44,
  "guinier_rg_error": 0.13,
  "pddf_dmax": 13.7,
  "pddf_dmax_error": null,
  "porod_volume": 360.0,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 10,
  "guinier_point_last": 35,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDB75_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
  "bragg_peak": []
}

{
  "code": "SASDB75",
  "status": "success",
  "started_at": "2026-08-11T14:40:48.155549+00:00",
  "finished_at": "2026-08-11T14:40:56.836766+00:00",
  "source_last_modified": "2019-12-06T13:07:15.624532+01:00",
  "files": [
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/rest-api/entry/summary/SASDB75/",
      "path": "/data/saxsdb/sasbdb/entries/75/sasdb75/source/summary.json",
      "size": 7786,
      "sha256": "79126cdb029c11155e9f81afc250c19226fcdb62d2b4ea7857fe6bcbfabf0b5c"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/intensities_files/SASDB75.dat",
      "path": "/data/saxsdb/sasbdb/entries/75/sasdb75/source/SASDB75.dat",
      "size": 20169,
      "sha256": "d5e75795ca7cda1aca7110848e564df635bc440c6b4519bd574e4474adcdb816",
      "role": "curve"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/p_of_R_files/SASDB75.out",
      "path": "/data/saxsdb/sasbdb/entries/75/sasdb75/source/SASDB75.out",
      "size": 35552,
      "sha256": "e60e99e6d297a1e63f24a2f4122b57972b2c391d2da48583ca6ac17a1fbc2884",
      "role": "pddf"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/sascif/sascif_files/SASDB75.sascif",
      "path": "/data/saxsdb/sasbdb/entries/75/sasdb75/source/SASDB75.sascif",
      "size": 222817,
      "sha256": "cec71008b1ea92a20f604ec7501c01d4cd45be399268ec853c0c5b451e7b5a3e",
      "role": "sascif"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/zip_directories/SASDB75.zip",
      "path": "/data/saxsdb/sasbdb/entries/75/sasdb75/source/SASDB75.zip",
      "size": 56679,
      "sha256": "286b2945ee3e6d8cbc0c7429db3ec11a01dcfe2e84e0cd4c9005cf199c48d5be",
      "role": "full_entry_zip",
      "zip_member_count": 6,
      "zip_validation": "central_directory_readable"
    }
  ]
}