{ "code": "SASDEB6", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/A", "project": { "title": "Functional and solution structure studies of amino sugar deacetylase and deaminase enzymes from Staphylococcus aureus.", "publication": { "title": "Functional and solution structure studies of amino sugar deacetylase and deaminase enzymes from Staphylococcus aureus.", "author_list": "Davies JS, Coombes D, Horne CR, Pearce FG, Friemann R, North RA, Dobson RCJ", "journal": "FEBS Lett", "doi": "10.1002/1873-3468.13289", "pmid": "30411345", "published_date": "2018 Nov 9" }, "status": "released", "submitted_date": "2018-10-09", "released_date": "2018-11-13" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEB6.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEB6.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEB6_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEB6_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEB6_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEB6_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEB6.sascif", "experiment": { "instrument": { "detector": { "type": "Dectris", "name": "Pilatus 1M", "resolution": 172.0 }, "name": "Australian Synchrotron", "city": "Melbourne", "country": "Australia", "beamline_name": "SAXS/WAXS", "beam_geometry": "Point", "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": "Glucosamine-6-phosphate deaminase", "short_name": null, "sequence": ">sp|A8YZR7|NAGB_STAAT Glucosamine-6-phosphate deaminase OS=Staphylococcus aureus (strain USA300 / TCH1516) OX=451516 GN=nagB PE=3 SV=1\r\nMKVLNLGSKKQASFYVACELYKEMAFNQHCKLGLATGGTMTDLYEQLVKLLNKNQLNVDN\r\nVSTFNLDEYVGLTASHPQSYHYYMDDMLFKQYPYFNRKNIHIPNGDADDMNAEASKYNDV\r\nLEQQGQRDIQILGIGENGHIGFNEPGTPFDSVTHIVDLTESTIKANSRYFKNEDDVPKQA\r\nISMGLANILQAKRIILLAFGEKKRAAITHLLNQEISVDVPATLLHKHPNVEIYLDDEACP\r\nKNVAKIHVDEMD", "organism": "Staphylococcus aureus", "uniprot_code": "A8YZR7", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MKVLNLGSKKQASFYVACELYKEMAFNQHCKLGLATGGTMTDLYEQLVKLLNKNQLNVDN\nVSTFNLDEYVGLTASHPQSYHYYMDDMLFKQYPYFNRKNIHIPNGDADDMNAEASKYNDV\nLEQQGQRDIQILGIGENGHIGFNEPGTPFDSVTHIVDLTESTIKANSRYFKNEDDVPKQA\nISMGLANILQAKRIILLAFGEKKRAAITHLLNQEISVDVPATLLHKHPNVEIYLDDEACP\nKNVAKIHVDEMD", "mw": 28.467, "total_mw": 56.934, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM Tris-HCl 150 mM NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "Staphylococcus aureus glucosamine-6-phosphate deaminase", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "New Zealand", "full_name": "University of Canterbury", "webpage": "https://www.canterbury.ac.nz/" } ], "contributor_name": "James", "contributor_surname": "Davies", "orcid": "https://orcid.org/0000-0003-4029-1650" } ], "concentration_method": null, "concentration_unit": null, "date": "2016-04-26", "storage_temperature": 4.0, "cell_temperature": 20.0, "exposure_time": 1.0, "number_of_frames": 999, "wavelength": 0.10332, "sample_detector_distance": 1.6, "concentration_min": null, "concentration_max": 6.0, "sample_volume": null, "flow_rate": null, "s_min": 0.121, "s_max": 6.866, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEB6_fit1_model1_img.png", "software": "PyMOL", "pdb_link": [ { "pdb_code": "1hot", "ext_code": "1HOT", "ext_type": "pdb", "difference_with_model": "derived" } ], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEB6_fit1_model1.pdb", "model_mw": 60.33, "bead_radius": null, "log": null, "symmetry": null, "comment": "Dimeric structure taken from the E. coli hexameric glucosamine-6-phosphate deaminase.", "user": 378 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/nagB_ecoli_Dimer1_fit_img.png", "software": "CRYSOL", "chi_square_value": 0.536, "p_value": 0.0, "fit_residual_plot": "nagB_ecoli_Dimer1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEB6_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Dimer1.log", "software_version": "ATSAS 2.8", "description": "" } ], "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 Staphylococcus aureus glucosamine-6-phosphate deaminase in 20 mM Tris-HCl, 150 mM NaCl, pH 8 were collected on the SAXS/WAXS beam line at the Australian Synchrotron (Melbourne, Australia) using a Dectris Pilatus 1M detector at a sample-detector distance of 1.6 m and at a wavelength of λ = 0.10332 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 6.00 mg/ml was measured at 20°C. 999 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": 56.4, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 53.0, "porod_mw_error": null, "pddf_i0": 0.06816, "pddf_i0_error": null, "guinier_i0": 0.0679, "guinier_i0_error": 0.0002, "pddf_rg": 2.75, "pddf_rg_error": null, "guinier_rg": 2.725, "guinier_rg_error": 0.031, "pddf_dmax": 8.92, "pddf_dmax_error": null, "porod_volume": 84.2, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 14, "guinier_point_last": 47, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDEB6_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }