{ "code": "SASDES6", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/A", "project": { "title": "The structure of the PA28-20S proteasome complex from Plasmodium falciparum and implications for proteostasis.", "publication": { "title": "The structure of the PA28-20S proteasome complex from Plasmodium falciparum and implications for proteostasis.", "author_list": "Xie SC, Metcalfe RD, Hanssen E, Yang T, Gillett DL, Leis AP, Morton CJ, Kuiper MJ, Parker MW, Spillman NJ, Wong W, Tsu C, Dick LR, Griffin MDW, Tilley L", "journal": "Nat Microbiol", "doi": "10.1038/s41564-019-0524-4", "pmid": "31384003", "published_date": "2019 Nov" }, "status": "released", "submitted_date": "2018-10-24", "released_date": "2019-08-02" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDES6.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDES6.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDES6_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDES6_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDES6_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDES6_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDES6.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": "Proteasome activator PA28", "short_name": "PA28", "sequence": "GMEAYLNKIDKIEPSDQKIKEEYNKFKYDITKQAIESLRERIPKRIIFFNNLVNVNSEPGSILNVNDLDGVSYKYKINKIEENVRKKHKGNNSSDFDEREKKKDSLDGHVKHFSNNEDSKLIIDDKVLYTHYVPSHKQIYLELEKIKTYASELIEIIGNIKLWIQLNVPRIEDGNNFGVGIQEEAIQELARVEESAFNLYDAIVKYYMERAKISTKVLKYPNVSDYQEAVRELDEKEWIHIKITIVDMRNNYIMLYDLLYKNWEKVVKPKNEDAHHRMTF", "organism": "Plasmodium falciparum", "uniprot_code": "Q8I374", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "heptamer", "molecular_type": "protein", "uniprot_sequence": "MEAYLNKIDKIEPSDQKIKEEYNKFKYDITKQAIESLRERIPKRIIFFNNLVNVNSEPGS\nILNVNDLDGVSYKYKINKIEENVRKKHKGNNSSDFDEREKKKDSLDGHVKHFSNNEDSKL\nIIDDKVLYTHYVPSHKQIYLELEKIKTYASELIEIIGNIKLWIQLNVPRIEDGNNFGVGI\nQEEAIQELARVEESAFNLYDAIVKYYMERAKISTKVLKYPNVSDYQEAVRELDEKEWIHI\nKITIVDMRNNYIMLYDLLYKNWEKVVKPKNEDAHHRMTF", "mw": 33.182, "total_mw": 232.274, "number_molecules": 7, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM Tris-HCl, 150 mM NaCl, 0.5 mM TCEP, 0.1% sodium azide", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.4, "deuteration": null }, "purity_method": null, "name": "The 11S subunit of the Plasmodium falciparum proteasome, PA28", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Melbourne, Australia", "full_name": "Bio21 Institute, The University of Melbourne", "webpage": "http://www.bio21.unimelb.edu.au/" } ], "contributor_name": "Riley D.", "contributor_surname": "Metcalfe", "orcid": "https://orcid.org/0000-0002-7154-780X" } ], "concentration_method": null, "concentration_unit": null, "date": "2017-12-02", "storage_temperature": null, "cell_temperature": 22.0, "exposure_time": 1.0, "number_of_frames": 10, "wavelength": 0.10332, "sample_detector_distance": 2.682, "concentration_min": null, "concentration_max": 10.0, "sample_volume": null, "flow_rate": null, "s_min": 0.053, "s_max": 3.356, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDES6_fit1_model1_img.png", "software": "CORAL", "pdb_link": [ { "pdb_code": "6dfk", "ext_code": "6DFK", "ext_type": "pdb", "difference_with_model": "derived" } ], "model_title": null, "type_of_model": "mix", "software_version": "CORAL05", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDES6_fit1_model1.pdb", "model_mw": 228.3, "bead_radius": 1.9, "log": null, "symmetry": "P7", "comment": "Model of the flexible regions of PfPA28. P7 symmetry in core and flexible regions.", "user": 380 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/run4-1_symmetric_ntRYVON_fit_img.png", "software": "CORAL", "chi_square_value": 5.56, "p_value": 0.0, "fit_residual_plot": "run4-1_symmetric_ntRYVON_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDES6_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/run4.log", "software_version": "CORAL05", "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDES6_fit2_model1_img.png", "software": "CORAL", "pdb_link": [ { "pdb_code": "6dfk", "ext_code": "6DFK", "ext_type": "pdb", "difference_with_model": "derived" } ], "model_title": null, "type_of_model": "mix", "software_version": "CORAL05", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDES6_fit2_model1.pdb", "model_mw": 228.3, "bead_radius": 1.9, "log": null, "symmetry": "P1", "comment": "Model of the flexible regions of PfPA28. P1 symmetry in flexible regions, P7 in core.", "user": 380 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/run3-1_assymetric_fit_img.png", "software": "CORAL", "chi_square_value": 4.69, "p_value": 0.0, "fit_residual_plot": "run3-1_assymetric_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDES6_fit2.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/run3_xNPF6I4.log", "software_version": "CORAL05", "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDES6_fit3_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/SASDES6_fit3_model1.pdb", "model_mw": null, "bead_radius": 1.9, "log": "https://www.sasbdb.org/media/log_files/g9_KkLLRoc.log", "symmetry": "P7", "comment": null, "user": 380 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/g9_HMLu18w_fit_img.png", "software": "GASBOR", "chi_square_value": 1.87, "p_value": 2.3e-05, "fit_residual_plot": "g9_HMLu18w_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDES6_fit3.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/g9_7kPop7p.log", "software_version": "2.3i", "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 the 11S subunit of the Plasmodium falciparum proteasome, PA28 in 20 mM Tris-HCl, 150 mM NaCl, 0.5 mM TCEP, 0.1% sodium azide, pH 7.4 were collected on the SAXS/WAXS beam line at the Australian Synchrotron (Melbourne, Australia) using a Pilatus 1M detector at a sample-detector distance of 2.7 m and at a wavelength of λ = 0.10332 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle; s-range = 0.05 < s < 3.34 nm-1). Co-flow operations were employed (Kirby et al., 2016, Acta Cryst. D 72(12): 1254–1266) to reduce radiation damage and allow higher X-ray flux onto the sample, and an optimized chromatography system to limit sample dilution. Data were collected following fractionation using an in-line size-exclusion chromatography column (Superdex 200 5/150 (GE Healthcare), at a flow rate of 0.45 mL/min, with the column pre-equilibrated in buffer. Data were collected using a 1.5 mm sample capillary at under continuous flow at 22°C, with SAXS data frames collected every second.", "tags": [], "intensity_unit": "1/cm", "experimental_mw": 263.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 302.0, "porod_mw_error": null, "pddf_i0": 0.2657, "pddf_i0_error": null, "guinier_i0": 0.27, "guinier_i0_error": 0.00019, "pddf_rg": 4.25, "pddf_rg_error": null, "guinier_rg": 4.326, "guinier_rg_error": 0.005, "pddf_dmax": 12.9, "pddf_dmax_error": null, "porod_volume": 484.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 12, "guinier_point_last": 64, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDES6_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }