{ "code": "SASDC28", "status": "Published", "type_of_curve": "Other", "angular_unit": "1/A", "project": { "title": "The atypical thiol-disulfide exchange protein α-DsbA2 from Wolbachia pipientis is a homotrimeric disulfide isomerase.", "publication": { "title": "The atypical thiol-disulfide exchange protein α-DsbA2 from Wolbachia pipientis is a homotrimeric disulfide isomerase.", "author_list": "Walden PM, Whitten AE, Premkumar L, Halili MA, Heras B, King GJ, Martin JL", "journal": "Acta Crystallogr D Struct Biol", "doi": "10.1107/S2059798318018442", "pmid": "30950399", "published_date": "2019 Mar 1" }, "status": "released", "submitted_date": "2017-10-03", "released_date": "2019-03-29" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDC28.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDC28.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC28_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC28_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDC28_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC28_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDC28.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": "DsbA-like disulfide oxidoreductase (thiol-disulfide exchange protein)", "short_name": "α-DsbA2", "sequence": "SNAMSLPIINNWLSNRSQMLNDDYIGEKLDNYISRNFDKIVKTLKEESIKSSYAARDNV\r\nTKSKISQYKDQIFDLTYPYSGNENSSVIAVGFLDYSCGHCKAIKNDIKQLINDGKIKYIFRDAPILGNAS\r\nLKAAKSALAVYFLNKEKYFDFHHAALSHKGEFSDESILDIVKNIGIDEDDFNDSIKDNADKIEQMINNSR\r\nLLVRDLGVGGTPFLIIGDSLFVGATDLNVLRKKVDELSHKQG", "organism": "Wolbachia endosymbiont of Drosophila melanogaster", "uniprot_code": "Q73FL6", "uniprot_range_first": 16, "uniprot_range_last": 252, "oligomerization": "trimer", "molecular_type": "protein", "uniprot_sequence": "MSRISFLLILIIAIASLPIINNWLSNRSQMLNDDYIGEKLDNYISRNFDKIVKTLKEESI\nKSSYAARDNVTKSKISQYKDQIFDLTYPYSGNENSSVIAVGFLDYSCGHCKAIKNDIKQL\nINDGKIKYIFRDAPILGNASLKAAKSALAVYFLDKEKYFDFHHAALSHKGEFSDESILDI\nVKNIGIDEDDFNDSIKDNADKIEQMINNSRLLVRDLGVGGTPFLIIGDSLFVGATDLNVL\nRKKVDELSHKQG", "mw": 27.071, "total_mw": 81.213, "number_molecules": 3, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "25 mM TRIS, 150 mM NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "Mature α-DsbA2 protein", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "ANSTO", "address": "Kirrawee DC, NSW 2232, Australia", "full_name": "Australian Nuclear Science and Technology Organisation", "webpage": "" } ], "contributor_name": "Andrew", "contributor_surname": "Whitten", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2014-03-29", "storage_temperature": 4.0, "cell_temperature": 20.0, "exposure_time": 5.0, "number_of_frames": 8, "wavelength": 0.1127, "sample_detector_distance": 1.575, "concentration_min": 0.35, "concentration_max": 1.15, "sample_volume": null, "flow_rate": null, "s_min": 0.103, "s_max": 3.992, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDC28_fit1_model1_img.png", "software": "DAMMIN", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "5.3", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDC28_fit1_model1.pdb", "model_mw": 52.625, "bead_radius": 2.5, "log": "https://www.sasbdb.org/media/log_files/damsel_0WumaPk.log", "symmetry": "P3", "comment": "Filtered model from Damaver", "user": 111 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDC28_fit1_fixed_fit_img.png", "software": "DAMMIN", "chi_square_value": 1.199, "p_value": 0.26545, "fit_residual_plot": "SASDC28_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDC28_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/run0_YE1wuMC.log", "software_version": "5.3", "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDC28_fit2_model1_img.png", "software": "CORAL", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDC28_fit2_model1.pdb", "model_mw": null, "bead_radius": 1.9, "log": null, "symmetry": "P3", "comment": "", "user": 111 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDC28_fit2_fixed_fit_img.png", "software": "CORAL", "chi_square_value": 1.37, "p_value": 0.0371, "fit_residual_plot": "SASDC28_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDC28_fit2.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/run10.log", "software_version": "1.1", "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "4.6", "i0_calibration_standard": null, "description": null, "experiment_description": "X-ray synchrotron radiation scattering data from the mature version of α-DsbA2 from Wolbachia pipientis in 25 mM TRIS 150mM NaCl pH 7.5 were collected on the SAXS/WAXS beam line of the Australian Synchrotron (Melbourne, Australia) in a SEC-SAXS configuration using a 2D Photon counting Pilatus 1M-W pixel detector (I(s) vs s, where s = 4π sin θ/λ and 2θ is the scattering angle; λ=0.1127 nm). Approximately 100 uL of 19.8 mg/ml protein solution were injected onto a WTC-030S5 column at a flow rate of 0.5 ml/min. Five hundred successive 5 second frames were collected during the SEC-SAXS run. The peak of the elution profile occured at ~18 mins after the start of the run, and the protein scattering was taken as the average of 8 frames collected 35-75 seconds after the peak eluted (the radius of gyration dropped to ~27.6 Ang at the peak concentration of ~2.2 mg/ml, so data was averaged at a region where the concentration was lower and concentration dependent effects were not apparent). The concentration range corresponding to the averaged frames was ~0.35 - 1.15 mg/ml, and the average concentration was taken as ~0.75 mg/ml. The buffer was taken as the sum of 100 frames collected between 3-9 mins after the start of the run. The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering of the solvent-blank was subtracted. The models and corresponding fits include those derived from dummy-atom modelling using DAMMIN (top) and rigid-body modelling using CORAL (bottom).", "tags": [], "intensity_unit": "1/cm", "experimental_mw": 86.7, "experimental_mw_error": null, "guinier_i0_mw": 86.7, "guinier_i0_mw_error": 5.0, "porod_mw": 75.0, "porod_mw_error": null, "pddf_i0": 0.04845, "pddf_i0_error": 2e-05, "guinier_i0": 0.04846, "guinier_i0_error": 3e-05, "pddf_rg": 2.79, "pddf_rg_error": 0.01, "guinier_rg": 2.8, "guinier_rg_error": 0.01, "pddf_dmax": 8.7, "pddf_dmax_error": 3.0, "porod_volume": 913.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 30, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDC28_datloglog_img.png", "symmetry": null, "last_modified": "2021-04-10T09:53:07.171187+02:00", "bragg_peak": [] }