{ "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 }, "fits": [ { "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, "description": "" } ], "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", "experimental_mw": 177.5, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 186.0, "porod_mw_error": null, "pddf_i0": 40.09, "pddf_i0_error": -2e-10, "guinier_i0": 39.4712, "guinier_i0_error": null, "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": [] }