Peroxisomal biogenesis factor 8 (Pex8) from P. pastoris

{
  "code": "SASDX94",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/nm",
  "project": {
    "title": "Structure of Pex8 in complex with peroxisomal receptor Pex5 reveals its essential role in peroxisomal cargo translocation",
    "publication": {
      "title": "Structure of Pex8 in complex with peroxisomal receptor Pex5 reveals its essential role in peroxisomal cargo translocation",
      "author_list": "Ekal L, Wendscheck D, David Y, Chojnowski G, Jeffries C, Mullapudi E, Schuldiner M, Warscheid B, Zalckvar E, Wilmanns M",
      "journal": null,
      "doi": "10.1101/2025.08.30.673231",
      "pmid": null,
      "published_date": "2025 Sep 02"
    },
    "status": "released",
    "submitted_date": "2025-04-25",
    "released_date": "2025-09-03"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDX94.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDX94.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX94_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX94_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDX94_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX94_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDX94.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": null,
        "name": "Pilatus 6M",
        "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": "Peroxisomal biogenesis factor 8",
          "short_name": "Pex8",
          "sequence": "GPMDMREAQRIPQQLDYLLAEIISPNEDTNVI\r\nGYLAYYYPKLKNEQNVALLTDFFLRCPTYFSHSNVVSLRNNYPVMEAFNYIMTTKFKVSQ\r\nPTVPFYRFYAAVLASLLNCEKTDPSHHWKLIPILTGVLLSIKGRDDVELYPDHSRSIKGS\r\nDTAVAQLLQRCLLRFYQSGDARSYDLNALVIISMSCALDYVEDDTIKKILYCFNYTRAII\r\nDLIYYSPYGLNDSDIPLLSDSSVNSQSFDQLLNNNPALKHLNRLSFLFERTVKLNDGSIQ\r\nSNLNDIDISLNKMQSFSEKLSKKISVLDDDSSKGVGQLLRQCLYASIIIHQAILTTFFQL\r\nDNADYTKYFLPSFSRKILSILFNLFFIVDRIGTGGFQPYNFVYLTCLQGIIQYDMKTAES\r\nLVKTFTTGINYSSLKDSEVARAKLLFTLNLMEQIVNICSDDLRLELIVPLVEDLVNNKNA\r\nCVDIHNHVFKSIFESAHSVILKFFTVVDSSVKNVDYETNVTLVSEKIIPYLTLVIDQFPE\r\nFLSINQLDIAIETISRTVFPDSPIYSYDKNISSMFLNVLFNKCLTVDNDELVELPAIEAV\r\nVAPKNDEENNTSDAQDGGPKELQSLNDLKSRRSALISALISVFPLIPVKDYTKWLSIAFY\r\nDLIVATPERTERAFLQERLWDCVVGTNKYDPQKGNLGIMWWYENVNAQSTAKL",
          "organism": "Komagataella pastoris",
          "uniprot_code": "Q01962",
          "uniprot_range_first": 33,
          "uniprot_range_last": 713,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MYRLGSQGRSIQSQLQNGDSSSGRPLQLQGTGMREAQRIPQQLDYLLAEIISPNEDTNVI\nGYLAYYYPKLKNEQNVALLTDFFLRCPTYFSHSNVVSLRNNYPVMEAFNYIMTTKFKVSQ\nPTVPFYRFYAAVLASLLNCEKTDPSHHWKLIPILTGVLLSIKGRDDVELYPDHSRSIKGS\nDTAVAQLLQRCLLRFYQSGDARSYDLNALVIISMSCALDYVEDDTIKKILYCFNYTRAII\nDLIYYSPYGLNDSDIPLLSDSSVNSQSFDQLLNNNPALKHLNRLSFLFERTVKLNDGSIQ\nSNLNDIDISLNKMQSFSEKLSKKISVLDDDSSKGVGQLLRQCLYASIIIHQAILTTFFQL\nDNADYTKYFLPSFSRKILSILFNLFFIVDRIGTGGFQPYNFVYLTCLQGIIQYDMKTAES\nLVKTFTTGINYSSLKDSEVARAKLLFTLNLMEQIVNICSDDLRLELIVPLVEDLVNNKNA\nCVDIHNHVFKSIFESAHSVILKFFTVVDSSVKNVDYETNVTLVSEKIIPYLTLVIDQFPE\nFLSINQLDIAIETISRTVFPDSPIYSYDKNISSMFLNVLFNKCLTVDNDELVELPAIEAV\nVAPKNDEENNTSDAQDGGPKELQSLNDLKSRRSALISALISVFPLIPVKDYTKWLSIAFY\nDLIVATPERTERAFLQERLWDCVVGTNKYDPQKGNLGIMWWYENVNAQSTAKL",
          "mw": 78.017,
          "total_mw": 78.017,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": "The protein construct used for SAXS contains an additional four non-native amino acids at the N-terminus (GPMD). The protein was expressed in E. coli BL21 DE3 Lobstr cells."
        }
      ],
      "buffer": {
        "name": "50 mM HEPES, 150 mM NaCl, 3% v/v glycerol",
        "concentration_unit": null,
        "comment": "0.2um filtered and degassed",
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Peroxisomal biogenesis factor 8 (Pex8) from P. pastoris",
      "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": "Lakhan",
        "contributor_surname": "Ekal",
        "orcid": "https://orcid.org/0000-0001-8916-4201"
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2021-08-17",
    "storage_temperature": 10.0,
    "cell_temperature": 20.0,
    "exposure_time": 0.5,
    "number_of_frames": 46,
    "wavelength": 0.123982,
    "sample_detector_distance": 3.0,
    "concentration_min": null,
    "concentration_max": 4.0,
    "sample_volume": 90.0,
    "flow_rate": 0.6,
    "s_min": 0.024,
    "s_max": 7.393,
    "total_exposure_time": null,
    "seccolumn": 1
  },
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    {
      "models": [
        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDX94_fit1_model1_img.png",
          "software": "MultiFoXS",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "atomic",
          "software_version": null,
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDX94_fit1_model1.pdb",
          "model_mw": 77.6,
          "bead_radius": null,
          "log": null,
          "symmetry": "P1",
          "comment": null,
          "user": 1019
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDX94_fit1_fixed_fit_img.png",
      "software": "MultiFoXS",
      "chi_square_value": 0.989,
      "p_value": 0.1358,
      "fit_residual_plot": "SASDX94_fit1_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDX94_fit1.fit",
      "fit_log": null,
      "software_version": null,
      "description": ""
    }
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  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": "5.0",
  "i0_calibration_standard": null,
  "description": "The experimental molecular weight was estimated using Bayesian inference in the MW rage of 67-75 kDa (datmw tool, ATSAS 3; GNOM.out file input). MultiFoXS modelling routines and the unsubtracted SEC-SAXS data frames are made available in the full entry zip archive.",
  "experiment_description": "Synchrotron SAXS data from solutions of Pex8 in 50 mM HEPES, 150 mM NaCl, 3% v/v glycerol, pH 7.5 were collected on the EMBL P12 beam line at PETRA III (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.123982 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 90.00 μl sample at 4 mg/ml was injected at a 0.60 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 20°C. 46 successive 0.500 second frames were collected through the main SEC elution peak. 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",
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  "experimental_mw_error": null,
  "guinier_i0_mw": null,
  "guinier_i0_mw_error": null,
  "porod_mw": 73.0,
  "porod_mw_error": null,
  "pddf_i0": 0.01762,
  "pddf_i0_error": null,
  "guinier_i0": 0.0174059,
  "guinier_i0_error": null,
  "pddf_rg": 3.755,
  "pddf_rg_error": null,
  "guinier_rg": 3.605,
  "guinier_rg_error": 0.015,
  "pddf_dmax": 13.0,
  "pddf_dmax_error": null,
  "porod_volume": 117.0,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 13,
  "guinier_point_last": 122,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDX94_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2025-09-03T12:12:25.993312+02:00",
  "bragg_peak": []
}

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  "finished_at": "2026-08-11T14:19:09.713709+00:00",
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