{ "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": [] }