{ "code": "SASDFD6", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/nm", "project": { "title": "Studying Conformational Changes of the Yersinia Type-III-Secretion Effector YopO in Solution by Integrative Structural Biology.", "publication": { "title": "Studying Conformational Changes of the Yersinia Type-III-Secretion Effector YopO in Solution by Integrative Structural Biology.", "author_list": "Peter MF, Tuukkanen AT, Heubach CA, Selsam A, Duthie FG, Svergun DI, Schiemann O, Hagelueken G", "journal": "Structure", "doi": "10.1016/j.str.2019.06.007", "pmid": "31303480", "published_date": "2019 Sep 3" }, "status": "released", "submitted_date": "2019-05-06", "released_date": "2019-09-11" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFD6.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFD6.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFD6_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFD6_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFD6_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFD6_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFD6.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 2M", "resolution": null }, "name": "PETRA III", "city": "DESY; Hamburg", "country": "Germany", "beamline_name": "EMBL P12", "beam_geometry": null, "type_of_source": "X-ray synchrotron", "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": "Protein kinase YopO", "short_name": "YopO", "sequence": 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"MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS\r\nKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT\r\nQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL\r\nAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY\r\nELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLS\r\nGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ\r\nEYDESGPSIVHRKCF", "organism": "Homo sapiens", "uniprot_code": "P60709", "uniprot_range_first": 1, "uniprot_range_last": 375, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS\nKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT\nQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL\nAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY\nELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLS\nGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ\nEYDESGPSIVHRKCF", "mw": 41.737, "total_mw": 41.737, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "10 mM Tris-HCl, 50 mM NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "Protein kinase YopO - cytoplasmic 1 actin complex", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "EMBL-Hamburg", "address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany", "full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation", "webpage": "http://www.embl-hamburg.de/index.php" } ], "contributor_name": "Anne", "contributor_surname": "Tuukkanen", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2017-05-06", "storage_temperature": 10.0, "cell_temperature": 20.0, "exposure_time": 1.0, "number_of_frames": 3600, "wavelength": 0.124, "sample_detector_distance": 3.0, "concentration_min": null, "concentration_max": 5.52, "sample_volume": 80.0, "flow_rate": null, "s_min": 0.133, "s_max": 7.267, "total_exposure_time": null, "seccolumn": 1 }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFD6_fit1_model1_img.png", "software": "Custom in-house", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDFD6_fit1_model1.pdb", "model_mw": 103.5, "bead_radius": null, "log": null, "symmetry": null, "comment": "PELDOR/SAXS refinement without clash penalty", "user": 27 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/617currentBest_000_n21qnQr_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 1.098, "p_value": 0.01337, "fit_residual_plot": "617currentBest_000_n21qnQr_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFD6_fit1.fit", "fit_log": null, "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFD6_fit2_model1_img.png", "software": "Custom in-house", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDFD6_fit2_model1.pdb", "model_mw": 103.5, "bead_radius": null, "log": null, "symmetry": null, "comment": "PELDOR/SAXS refinement with clash penalty", "user": 27 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/616_currentBest_000_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 1.123, "p_value": 0.003355, "fit_residual_plot": "616_currentBest_000_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFD6_fit2.fit", "fit_log": null, "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFD6_fit3_model1_img.png", "software": "Custom in-house", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDFD6_fit3_model1.pdb", "model_mw": 103.5, "bead_radius": null, "log": null, "symmetry": null, "comment": "Model ignoring the Kinase 113 – Actin 374 restraint", "user": 27 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/621_currentBest_000_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 1.075, "p_value": 0.01337, "fit_residual_plot": "621_currentBest_000_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFD6_fit3.fit", "fit_log": null, "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": "Synchrotron SAXS data from solutions of protein kinase YopO in complex with actin in 10 mM Tris-HCl, 50 mM NaCl, pH 8 were collected on the EMBL P12 beam line at the PETRA III (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAXS was employed. The SEC parameters were as follows: A 80.00 μl sample at 5.5 mg/ml was injected onto a GE Superdex 200 Increase 10/300 column at 20°C. 3600 successive 1 second frames were collected through the SEC elution. The data from the sample peak 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": 109.1, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 82.1, "porod_mw_error": null, "pddf_i0": 615.1, "pddf_i0_error": 3.1, "guinier_i0": 611.0, "guinier_i0_error": 1.0, "pddf_rg": 3.658, "pddf_rg_error": null, "guinier_rg": 3.6, "guinier_rg_error": 0.1, "pddf_dmax": 12.33, "pddf_dmax_error": 0.6, "porod_volume": 147.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 84, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDFD6_datloglog_img.png", "symmetry": null, "last_modified": "2023-06-21T07:56:39.492710+02:00", "bragg_peak": [] }