Aspergillus niger beta-glucosidase (bgl1), partially deglycosylated with Endoglycosidase H

{
  "code": "SASDUX7",
  "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/SASDUX7.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDUX7.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUX7_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUX7_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDUX7_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUX7_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDUX7.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), partially deglycosylated with Endoglycosidase H",
      "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": "2024-02-15",
    "storage_temperature": 4.0,
    "cell_temperature": null,
    "exposure_time": 2.0,
    "number_of_frames": 10,
    "wavelength": 0.08189,
    "sample_detector_distance": 3.562,
    "concentration_min": null,
    "concentration_max": 4.5,
    "sample_volume": 99.0,
    "flow_rate": 0.35,
    "s_min": 0.06,
    "s_max": 31.9,
    "total_exposure_time": null,
    "seccolumn": 42
  },
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    {
      "models": [
        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDUX7_fit1_model1_img.png",
          "software": "GASBOR",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "dummy",
          "software_version": null,
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDUX7_fit1_model1.cif",
          "model_mw": null,
          "bead_radius": null,
          "log": "https://www.sasbdb.org/media/log_files/Dammin-slow-9.log",
          "symmetry": "P1",
          "comment": null,
          "user": 889
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDUX7_fit1_fixed_fit_img.png",
      "software": "GASBOR",
      "chi_square_value": 2.39,
      "p_value": 0.0,
      "fit_residual_plot": "SASDUX7_fit1_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDUX7_fit1.fir",
      "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Dammin-slow-9.log",
      "software_version": null,
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  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": "5.0",
  "i0_calibration_standard": null,
  "description": "For the experiment, SAXS and WAXS detectors were used simultaneously. The detector positions are Sample-to-detector distance (in meters): SAXS - 3.562, WAXS - 0.317",
  "experiment_description": "Synchrotron SAXS data from solutions of Aspergillus niger beta-glucosidase (bgl1) 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 detector at a sample-detector distance of 3.6 m and 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 99.00 μl sample at 4.5 mg/ml was injected at a 0.35 ml/min flow rate onto a Biozen 3 µm dSEC-2, 200 Å column. 10 successive 2-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",
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  "experimental_mw_error": null,
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  "guinier_i0_mw_error": null,
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  "porod_mw_error": null,
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  "pddf_i0_error": -2e-10,
  "guinier_i0": 39.4712,
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  "pddf_rg": 4.37,
  "pddf_rg_error": null,
  "guinier_rg": 4.24,
  "guinier_rg_error": 0.193,
  "pddf_dmax": 14.0,
  "pddf_dmax_error": null,
  "porod_volume": 253.0,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 1,
  "guinier_point_last": 24,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDUX7_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2024-06-14T16:27:53.242047+02:00",
  "bragg_peak": []
}

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  "finished_at": "2026-08-11T15:42:21.960531+00:00",
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