Full-length X-chromosome linked inhibitor of apoptosis protein (XIAP)

{
  "code": "SASDF24",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/nm",
  "project": {
    "title": "Conformational characterization of full-length X-chromosome-linked inhibitor of apoptosis protein (XIAP) through an integrated approach.",
    "publication": {
      "title": "Conformational characterization of full-length X-chromosome-linked inhibitor of apoptosis protein (XIAP) through an integrated approach.",
      "author_list": "Polykretis P, Luchinat E, Bonucci A, Giachetti A, Graewert MA, Svergun DI, Banci L",
      "journal": "IUCrJ",
      "doi": "10.1107/S205225251901073X",
      "pmid": "31576227",
      "published_date": "2019 Sep 1"
    },
    "status": "released",
    "submitted_date": "2019-03-14",
    "released_date": "2019-08-28"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDF24.out",
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  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF24_kratky_img.png",
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  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF24_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDF24.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": null,
        "name": "Pilatus 2M",
        "resolution": null
      },
      "name": "PETRA III",
      "city": "DESY; Hamburg",
      "country": "Germany",
      "beamline_name": "EMBL P12",
      "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": "E3 ubiquitin-protein ligase XIAP",
          "short_name": null,
          "sequence": "MTFNSFEGSKTCVPADINKEEEFVEEFNRLKTFANFPSGSPVSASTLARAGFLYTGEGDT\r\nVRCFSCHAAVDRWQYGDSAVGRHRKVSPNCRFINGFYLENSATQSTNSGIQNGQYKVENY\r\nLGSRDHFALDRPSETHADYLLRTGQVVDISDTIYPRNPAMYSEEARLKSFQNWPDYAHLT\r\nPRELASAGLYYTGIGDQVQCFCCGGKLKNWEPCDRAWSEHRRHFPNCFFVLGRNLNIRSE\r\nSDAVSSDRNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKC\r\nFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLEECLVRTTEKTP\r\nSLTRRIDDTIFQNPMVQEAIRMGFSFKDIKKIMEEKIQISGSNYKSLEVLVADLVNAQKD\r\nSMQDESSQTSLQKEISTEEQLRRLQEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEAVDK\r\nCPMCYTVITFKQKIFMS",
          "organism": "Homo sapiens",
          "uniprot_code": "P98170",
          "uniprot_range_first": 1,
          "uniprot_range_last": 497,
          "oligomerization": "dimer",
          "molecular_type": "protein",
          "uniprot_sequence": "MTFNSFEGSKTCVPADINKEEEFVEEFNRLKTFANFPSGSPVSASTLARAGFLYTGEGDT\nVRCFSCHAAVDRWQYGDSAVGRHRKVSPNCRFINGFYLENSATQSTNSGIQNGQYKVENY\nLGSRDHFALDRPSETHADYLLRTGQVVDISDTIYPRNPAMYSEEARLKSFQNWPDYAHLT\nPRELASAGLYYTGIGDQVQCFCCGGKLKNWEPCDRAWSEHRRHFPNCFFVLGRNLNIRSE\nSDAVSSDRNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKC\nFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLEECLVRTTEKTP\nSLTRRIDDTIFQNPMVQEAIRMGFSFKDIKKIMEEKIQISGSNYKSLEVLVADLVNAQKD\nSMQDESSQTSLQKEISTEEQLRRLQEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEAVDK\nCPMCYTVITFKQKIFMS",
          "mw": 56.684,
          "total_mw": 113.368,
          "number_molecules": 2,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "Xiap buffer",
        "concentration_unit": null,
        "comment": "20 mM Tris buffer, 0.5 mM TCEP,",
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.4,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Full-length X-chromosome linked inhibitor of apoptosis protein (XIAP)",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": "EMBL-Hamburg",
            "address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
            "full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
            "webpage": "http://www.embl-hamburg.de/index.php"
          }
        ],
        "contributor_name": "Melissa ",
        "contributor_surname": "Graewert",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2017-09-15",
    "storage_temperature": null,
    "cell_temperature": 20.0,
    "exposure_time": 1.0,
    "number_of_frames": 15,
    "wavelength": 0.124,
    "sample_detector_distance": 3.0,
    "concentration_min": null,
    "concentration_max": 7.5,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.091,
    "s_max": 5.064,
    "total_exposure_time": null,
    "seccolumn": null
  },
  "fits": [
    {
      "models": [
        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF24_fit1_model1_img.png",
          "software": "HADDOCK",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "atomic",
          "software_version": null,
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDF24_fit1_model1.pdb",
          "model_mw": 114.0,
          "bead_radius": null,
          "log": null,
          "symmetry": null,
          "comment": null,
          "user": 14
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/testGR1_372700_fixed_fit_img.png",
      "software": "CRYSOL",
      "chi_square_value": 1.528,
      "p_value": 5.3e-05,
      "fit_residual_plot": "testGR1_372700_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF24_fit1.fit",
      "fit_log": null,
      "software_version": null,
      "description": "A number of models were gennerated using HADDOCK (van Zundert, G. C. P. et al. The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. J. Mol. Biol. 428, 720–725 (2016).\r\nThese were screened against the SAXS data using Crysol. The model with the best fit is shown here.\r\nModel input: starting from the atomic structures of the individual domains: BIR1 (2POI.pdb), BIR2 (1I3O.pdb), BIR3 (5M6E.pdb), UBA (2KNA.pdb) and RING (5O6T.pdb)."
    }
  ],
  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": "5.0",
  "i0_calibration_standard": null,
  "description": null,
  "experiment_description": "Synchrotron SAXS data from solutions of X-chromosome linked inhibitor of apoptosis protein (XIAP) in Xiap buffer, pH 7.4 were collected using size-exclusion chromatography SAXS (SEC-SAXS) on the EMBL P12 beam line at PETRA III (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). SEC-SAXS was performed at 20 °C using the following parameters: Column: Superdex 200 10/300 GL (GE healthcare Life Sciences); Flow rate: 0.5 mL/min; Sample injection concentration: 7.5 mg/mL; Injection volume: 100 μL. The data were collected through the SEC peak of the protein as a series of 15 x 1 second exposures. Each unsubtracted data frame was normalised to the intensity of the transmitted beam and radially averaged and the scattering of an appropriate solvent-blank was subtracted. The resulting subtracted frames were scaled and averaged to generate the final SAXS profile displayed in this entry.",
  "tags": [],
  "intensity_unit": "arbitrary",
  "experimental_mw": 115.0,
  "experimental_mw_error": null,
  "guinier_i0_mw": 0.0,
  "guinier_i0_mw_error": null,
  "porod_mw": 130.0,
  "porod_mw_error": null,
  "pddf_i0": 16800.0,
  "pddf_i0_error": null,
  "guinier_i0": 16438.0,
  "guinier_i0_error": 32.0,
  "pddf_rg": 3.99,
  "pddf_rg_error": null,
  "guinier_rg": 3.86,
  "guinier_rg_error": 0.06,
  "pddf_dmax": 12.82,
  "pddf_dmax_error": null,
  "porod_volume": 207.0,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 34,
  "guinier_point_last": 89,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDF24_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2023-06-21T07:56:39.492710+02:00",
  "bragg_peak": []
}

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