{ "code": "SASDGC6", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/A", "project": { "title": "The structural basis of fungal glucuronoyl esterase activity on natural substrates.", "publication": { "title": "The structural basis of fungal glucuronoyl esterase activity on natural substrates.", "author_list": "Ernst HA, Mosbech C, Langkilde AE, Westh P, Meyer AS, Agger JW, Larsen S", "journal": "Nat Commun", "doi": "10.1038/s41467-020-14833-9", "pmid": "32094331", "published_date": "2020 Feb 24" }, "status": "released", "submitted_date": "2019-09-27", "released_date": "2020-02-28" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDGC6.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDGC6.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGC6_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGC6_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDGC6_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGC6_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDGC6.sascif", "experiment": { "instrument": { "detector": { "type": "pixel counting", "name": "Pilatus3 R 300K", "resolution": 172.0 }, "name": "University of Copenhagen, Department of Drug Design and Pharmacology", "city": "Copenhagen", "country": "Denmark", "beamline_name": "Xenocs BioXolver L with GeniX3D", "beam_geometry": null, "type_of_source": "X-ray in house", "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": "4-O-methyl-glucuronoyl methylesterase (Glucuronoyl esterase)", "short_name": "CuGE", "sequence": ">FL_CuGE/1-481\r\nMQASAPQWGQCGGIGWTGPTACPSGWACQQLNAYYSQCLQGAAPAPARTTAAPPPPPATTAAPPPPTTSAPT\r\nGSSPVAGACGAIASTVPNYNNAKLPDPFTFANGTALRTKADWSCRRAEISALIQNYEAGTLPPKPPVVTASF\r\nSKSGNTGTLAITAGLSNSQTIKFSPTISYPSGTPPANGWPLIIAYEGGSIPIPAGVATLTYSNSDMAQQNSA\r\nSSRGQGLFYQLYGSTHSASAMTAWVWGVSRIIDALEMTPTAQINTQRIGVTGCSRDGKGALMAGAFEERIAL\r\nTIPQESGSGGDACWRLSKYEIDNGNQVQDAVEIVGENVWFSTNFNNYVQKLPTVPEDHHLLAAMVAPRAMIS\r\nFENTDYLWLSPMSSFGCMTAAHTVWQGLGIADSHGFAQVGGHAHCAWPSSLTPQLNAFINRFLLDQSATTNV\r\nFTTNNQFGKVQWNAANWITWTTPTLTGLEQKLISEEDLNSAVDHHHHHH", "organism": "Cerrena unicolor", "uniprot_code": "A0A0A7EQR3", "uniprot_range_first": 18, "uniprot_range_last": 474, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MFKPSFVALALVSYATAQASAPQWGQCGGIGWTGPTACPSGWACQQLNAYYSQCLQGAAP\nAPARTTAAPPPPPATTAAPPPPTTSAPTGSSPVAGACGAIASTVPNYNNAKLPDPFTFAN\nGTALRTKADWSCRRAEISALIQNYEAGTLPPKPPVVTASFSKSGNTGTLAITAGLSNSQT\nIKFSPTISYPSGTPPANGWPLIIAYEGGSIPIPAGVATLTYSNSDMAQQNSASSRGQGLF\nYQLYGSTHSASAMTAWVWGVSRIIDALEMTPTAQINTQRIGVTGCSRDGKGALMAGAFEE\nRIALTIPQESGSGGDACWRLSKYEIDNGNQVQDAVEIVGENVWFSTNFNNYVQKLPTVPE\nDHHLLAAMVAPRAMISFENTDYLWLSPMSSFGCMTAAHTVWQGLGIADSHGFAQVGGHAH\nCAWPSSLTPQLNAFINRFLLDQSATTNVFTTNNQFGKVQWNAANWITWTTPTLT", "mw": 50.907, "total_mw": 50.907, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM sodium acetate", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 5.0, "deuteration": null }, "purity_method": null, "name": "Glucuronoyl esterase, deglycolsylated full length", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Copenhagen, Denmark", "full_name": "University of Copenhagen", "webpage": "http://www.ku.dk/" } ], "contributor_name": "Annette", "contributor_surname": "Langkilde", "orcid": "" } ], "concentration_method": null, "concentration_unit": null, "date": "2018-10-10", "storage_temperature": 21.0, "cell_temperature": 21.0, "exposure_time": 60.0, "number_of_frames": 10, "wavelength": 0.154, "sample_detector_distance": 0.571, "concentration_min": null, "concentration_max": 3.7, "sample_volume": null, "flow_rate": null, "s_min": 0.197, "s_max": 4.805, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDGC6_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/SASDGC6_fit1_model1.pdb", "model_mw": 46.714, "bead_radius": 2.25, "log": "https://www.sasbdb.org/media/log_files/sub_012.log", "symmetry": "P1", "comment": null, "user": 42 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDGC6_fit1_fixed_fit_img.png", "software": "DAMMIN", "chi_square_value": 1.109, "p_value": 0.774734, "fit_residual_plot": "SASDGC6_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDGC6_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/sub_012.log", "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDGC6_fit2_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/SASDGC6_fit2_model1.pdb", "model_mw": null, "bead_radius": 1.9, "log": "https://www.sasbdb.org/media/log_files/sub012-gasbori.log", "symmetry": "P1", "comment": null, "user": 42 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDGC6_fit2_fixed_fit_img.png", "software": "GASBOR", "chi_square_value": 1.17, "p_value": 0.00215, "fit_residual_plot": "SASDGC6_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDGC6_fit2.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/sub012-gasbori.log", "software_version": null, "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": null, "experiment_description": "SAXS data from solutions of full-length deglycolsylated glucuronoyl esterase in 20 mM sodium acetate, pH 5 were collected using a Xenocs BioXolver L with GeniX3D (University of Copenhagen, Department of Drug Design and Pharmacology) equipped with a Pilatus3 R 300K detector at a sample-detector distance of 0.6 m and at a wavelength of λ = 0.154 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.70 mg/ml was measured at 21°C. 10 successive 60 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": 45.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 44.0, "porod_mw_error": null, "pddf_i0": 0.05964, "pddf_i0_error": null, "guinier_i0": 0.062, "guinier_i0_error": 0.00093, "pddf_rg": 3.19, "pddf_rg_error": null, "guinier_rg": 3.19, "guinier_rg_error": 0.29, "pddf_dmax": 11.0, "pddf_dmax_error": null, "porod_volume": 71.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 2, "guinier_point_last": 18, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDGC6_datloglog_img.png", "symmetry": null, "last_modified": "2020-11-03T10:09:09.624639+01:00", "bragg_peak": [] }