Aspergillus niger beta-glucosidase (bgl1), native, glycosylated

{
  "code": "SASDV52",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/A",
  "project": {
    "title": "Aspergillus niger beta-glucosidase (bgl1)",
    "publication": null,
    "status": "released",
    "submitted_date": "2024-04-24",
    "released_date": "2024-04-30"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDV52.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDV52.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDV52_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDV52_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/PTBP2_0284-0287s-new_kkEgYT3_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDV52_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDV52.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": "duel detector",
        "name": "Pilatus3 X 1M , Pilatus3 X 900K",
        "resolution": null
      },
      "name": "National Synchrotron Light Source II (NSLS-II)",
      "city": "Upton, NY",
      "country": "USA",
      "beamline_name": "16-ID (LiX)",
      "beam_geometry": null,
      "type_of_source": "X-ray synchrotron",
      "point_source": true,
      "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": "beta-glucosidase",
          "short_name": "bgl1",
          "sequence": "MRFTLIEAVALTAVSLASADELAYSPPYYPSPWANGQGDWAQAYQRAVDIVSQMTLDEKVNLTTGTGWELELCVGQTGGVPRLGVPGMCLQDSPLGVRDSDYNSAFPAGMNVAATWDKNLAYLRGKAMGQEFSDKGADIQLGPAAGPLGRSPDGGRNWEGFSPDPALSGVLFAETIKGIQDAGVVATAKHYIAYEQEHFRQAPEAQGFGFNISESGSANLDDKTMHELYLWPFADAIRAGAGAVMCSYNQINNSYGCQNSYTLNKLLKAELGFQGFVMSDWAAHHAGVSGALAGLDMSMPGDVDYDSGTSYWGTNLTISVLNGTVPQWRVDDMAVRIMAAYYKVGRDRLWTPPNFSSWTRDEYGYKYYYVSEGPYEKVNQYVNVQRNHSELIRRIGADSTVLLKNDGALPLTGKERLVALIGEDAGSNPYGANGCSDRGCDNGTLAMGWGSGTANFPYLVTPEQAISNEVLKHKNGVFTATDNWAIDQIEALAKTASVSLVFVNADSGEGYINVDGNLGDRRNLTLWRNGDNVIKAAASNCNNTIVVIHSVGPVLVNEWYDNPNVTAILWGGLPGQESGNSLADVLYGRVNPGAKSPFTWGKTREAYQDYLVTEPNNGNGAPQEDFVEGVFIDYRGFDKRNETPIYEFGYGLSYTTFNYSNLEVQVLSAPAYEPASGETEAAPTFGEVGNASDYLYPSGLQRITKFIYPWLNGTDLEASSGDASYGQDSSDYLPEGATDGSAQPILPAGGGPGGNPRLYDELIRVSVTIKNTGKVAGDEVPQLYVSLGGPNEPKIVLRQFERITLQPSEETKWSTTLTRRDLANWNVEKQDWEITSYPKMVFVGSSSRKLPLRASLPTVH",
          "organism": "Aspergillus niger",
          "uniprot_code": "Q9P8F4",
          "uniprot_range_first": 1,
          "uniprot_range_last": 860,
          "oligomerization": "dimer",
          "molecular_type": "protein",
          "uniprot_sequence": "MRFTLIEAVALTAVSLASADELAYSPPYYPSPWANGQGDWAQAYQRAVDIVSQMTLDEKV\nNLTTGTGWELELCVGQTGGVPRLGVPGMCLQDSPLGVRDSDYNSAFPAGMNVAATWDKNL\nAYLRGKAMGQEFSDKGADIQLGPAAGPLGRSPDGGRNWEGFSPDPALSGVLFAETIKGIQ\nDAGVVATAKHYIAYEQEHFRQAPEAQGFGFNISESGSANLDDKTMHELYLWPFADAIRAG\nAGAVMCSYNQINNSYGCQNSYTLNKLLKAELGFQGFVMSDWAAHHAGVSGALAGLDMSMP\nGDVDYDSGTSYWGTNLTISVLNGTVPQWRVDDMAVRIMAAYYKVGRDRLWTPPNFSSWTR\nDEYGYKYYYVSEGPYEKVNQYVNVQRNHSELIRRIGADSTVLLKNDGALPLTGKERLVAL\nIGEDAGSNPYGANGCSDRGCDNGTLAMGWGSGTANFPYLVTPEQAISNEVLKHKNGVFTA\nTDNWAIDQIEALAKTASVSLVFVNADSGEGYINVDGNLGDRRNLTLWRNGDNVIKAAASN\nCNNTIVVIHSVGPVLVNEWYDNPNVTAILWGGLPGQESGNSLADVLYGRVNPGAKSPFTW\nGKTREAYQDYLVTEPNNGNGAPQEDFVEGVFIDYRGFDKRNETPIYEFGYGLSYTTFNYS\nNLEVQVLSAPAYEPASGETEAAPTFGEVGNASDYLYPSGLQRITKFIYPWLNGTDLEASS\nGDASYGQDSSDYLPEGATDGSAQPILPAGGGPGGNPRLYDELIRVSVTIKNTGKVAGDEV\nPQLYVSLGGPNEPKIVLRQFERITLQPSEETKWSTTLTRRDLANWNVEKQDWEITSYPKM\nVFVGSSSRKLPLRASLPTVH",
          "mw": 93.345,
          "total_mw": 186.69,
          "number_molecules": 2,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": "Purified protein from native Aspergillus niger glucosidase crude product."
        }
      ],
      "buffer": {
        "name": "50 mM sodium acetate",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 5.0,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Aspergillus niger beta-glucosidase (bgl1), native, glycosylated",
      "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": "Brookhaven National Laboratory",
            "webpage": null
          }
        ],
        "contributor_name": "Estella",
        "contributor_surname": "Yee",
        "orcid": "https://orcid.org/0000-0001-7108-1387"
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2024-06-04",
    "storage_temperature": 4.0,
    "cell_temperature": null,
    "exposure_time": 1.0,
    "number_of_frames": 5,
    "wavelength": 0.08189,
    "sample_detector_distance": 4.003,
    "concentration_min": null,
    "concentration_max": 9.5,
    "sample_volume": 54.0,
    "flow_rate": 0.35,
    "s_min": 0.06,
    "s_max": 31.9,
    "total_exposure_time": null,
    "seccolumn": 2
  },
  "fits": [
    {
      "models": [
        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDV52_fit1_model1_img.png",
          "software": "DAMMIN",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "dummy",
          "software_version": null,
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDV52_fit1_model1.cif",
          "model_mw": null,
          "bead_radius": null,
          "log": "https://www.sasbdb.org/media/log_files/dammin-slow-8.log",
          "symmetry": "P1",
          "comment": "Dammin was run on the most representative model of 10 generated by GASBOR.",
          "user": 889
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDV52_fit1_fixed_fit_img.png",
      "software": "DAMMIN",
      "chi_square_value": 0.719,
      "p_value": 0.5363,
      "fit_residual_plot": "SASDV52_fit1_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDV52_fit1.fir",
      "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/dammin-slow-8_zAp32QL.log",
      "software_version": null,
      "description": "Dammin was run on the most representative model of 10 generated by GASBOR."
    }
  ],
  "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 Aspergillus niger beta-glucosidase (bgl1), native, glycosylated in 50 mM sodium acetate, pH 5 were collected on the 16-ID (LiX) beamline at the National Synchrotron Light Source II (NSLS-II) storage ring (Upton, NY, USA) using a Pilatus3 X 1M, Pilatus3 X 900K dual detectors at a sample-detector distance of 4.003 m (SAXS) and 0.282 m (WAXS) at a wavelength of λ = 0.08189 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 54.00 μl sample at 9.5 mg/ml was injected at a 0.35 ml/min flow rate onto a GE Superdex 200 Increase 5/150 column. Five successive 1 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": "arbitrary",
  "experimental_mw": 195.2,
  "experimental_mw_error": null,
  "guinier_i0_mw": null,
  "guinier_i0_mw_error": null,
  "porod_mw": 230.0,
  "porod_mw_error": null,
  "pddf_i0": 24.93,
  "pddf_i0_error": -2e-10,
  "guinier_i0": 24.8383,
  "guinier_i0_error": null,
  "pddf_rg": 4.45,
  "pddf_rg_error": null,
  "guinier_rg": 4.396,
  "guinier_rg_error": 0.166,
  "pddf_dmax": 13.9,
  "pddf_dmax_error": null,
  "porod_volume": 277.0,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 3,
  "guinier_point_last": 24,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDV52_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2024-07-02T12:09:46.992729+02:00",
  "bragg_peak": []
}

{
  "code": "SASDV52",
  "status": "success",
  "started_at": "2026-08-11T13:31:03.446456+00:00",
  "finished_at": "2026-08-11T13:31:10.411332+00:00",
  "source_last_modified": "2024-07-02T12:09:46.992729+02:00",
  "files": [
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/rest-api/entry/summary/SASDV52/",
      "path": "/data/saxsdb/sasbdb/entries/52/sasdv52/source/summary.json",
      "size": 8861,
      "sha256": "f494ee724f4d932418760f1b672bf68ed9bc70ccaf572727c7c65d3d4a733a86"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/intensities_files/SASDV52.dat",
      "path": "/data/saxsdb/sasbdb/entries/52/sasdv52/source/SASDV52.dat",
      "size": 9009,
      "sha256": "6fa0df8ddfd9d3de53fa309b4f7f1ba69d6e941817857b1414bbb4f3451347ff",
      "role": "curve"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/p_of_R_files/SASDV52.out",
      "path": "/data/saxsdb/sasbdb/entries/52/sasdv52/source/SASDV52.out",
      "size": 22196,
      "sha256": "48db4d32a3aa02fd70cc349ef1bdd3a1c68f88b8685a3761e80aa1bd5f2f5e30",
      "role": "pddf"
    },
    {
      "status": "not_available",
      "url": "https://www.sasbdb.org/media/sascif/sascif_files/SASDV52.sascif",
      "path": "/data/saxsdb/sasbdb/entries/52/sasdv52/source/SASDV52.sascif",
      "role": "sascif"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/zip_directories/SASDV52.zip",
      "path": "/data/saxsdb/sasbdb/entries/52/sasdv52/source/SASDV52.zip",
      "size": 22175,
      "sha256": "cbfcae980c548c898391daffc9e6289d6987b026b91ac4cee9e3565a5e45831c",
      "role": "full_entry_zip",
      "zip_member_count": 4,
      "zip_validation": "central_directory_readable"
    }
  ]
}