{ "code": "SASDFE5", "status": "Published", "type_of_curve": "Merged", "angular_unit": "1/nm", "project": { "title": "Thermodynamics, cooperativity and stability of the tetracycline repressor (TetR) upon tetracycline binding.", "publication": { "title": "Thermodynamics, cooperativity and stability of the tetracycline repressor (TetR) upon tetracycline binding.", "author_list": "Palm GJ, Buchholz I, Werten S, Girbardt B, Berndt L, Delcea M, Hinrichs W", "journal": "Biochim Biophys Acta Proteins Proteom", "doi": "10.1016/j.bbapap.2020.140404", "pmid": "32114262", "published_date": "2020 Feb 27" }, "status": "released", "submitted_date": "2019-04-11", "released_date": "2020-03-05" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFE5.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFE5.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFE5_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFE5_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFE5_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFE5_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFE5.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": "Tetracycline repressor (class D)", "short_name": "TetR(D)", "sequence": "SRLNRESVIDAALELLNETGIDGLTTRKLAQKLGIEQPTLYWHVKNKRALLDALAVEILARHHDYSLPAAGESWQSFLRNNAMSFRRALLRYRDGAKVHLGTRPDEKQYDTVETQLRFMTENGFSLRDGLYAISAVSHFTLGAVLEQQEHTAALTDRPAAPDENLPPLLREALQIMDSDDGEQAFLHGLESLIRGFEVQLTALLQIV", "organism": "Escherichia coli", "uniprot_code": "P0ACT4", "uniprot_range_first": 2, "uniprot_range_last": 208, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MARLNRESVIDAALELLNETGIDGLTTRKLAQKLGIEQPTLYWHVKNKRALLDALAVEIL\nARHHDYSLPAAGESWQSFLRNNAMSFRRALLRYRDGAKVHLGTRPDEKQYDTVETQLRFM\nTENGFSLRDGLYAISAVSHFTLGAVLEQQEHTAALTDRPAAPDENLPPLLREALQIMDSD\nDGEQAFLHGLESLIRGFEVQLTALLQIVGGDKLIIPFC", "mw": 23.259, "total_mw": 46.518, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "5a,6-anhydrotetracycline", "short_name": "ATc", "sequence": "C22H22N2O7", "organism": null, "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "dimer", "molecular_type": "other", "uniprot_sequence": null, "mw": 0.426, "total_mw": 0.852, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50 mM Tris/HCl 150 mM NaCl 10 mM MgCl2", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "Tetracycline repressor (class D), TetR(D), in complex with 5a,6-anhydrotetracycline (ATc)", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Innsbruck, Austria", "full_name": "Medical University of Innsbruck", "webpage": "https://www.i-med.ac.at/" } ], "contributor_name": "Sebastiaan", "contributor_surname": "Werten", "orcid": "https://orcid.org/0000-0003-2244-9688" } ], "concentration_method": null, "concentration_unit": null, "date": "2013-09-23", "storage_temperature": null, "cell_temperature": 10.0, "exposure_time": 0.05, "number_of_frames": 20, "wavelength": 0.124, "sample_detector_distance": 3.1, "concentration_min": 1.35, "concentration_max": 1.35, "sample_volume": null, "flow_rate": null, "s_min": 0.06, "s_max": 4.458, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFE5_fit1_model1_img.png", "software": "PDB (Protein Data Bank)", "pdb_link": [ { "pdb_code": "4d7m", "ext_code": "4D7M", "ext_type": "pdb", "difference_with_model": "other" } ], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDFE5_fit1_model1.pdb", "model_mw": 47.87, "bead_radius": null, "log": null, "symmetry": "p2", "comment": "A dimer was generated from the PDB entry by applying crystallographic symmetry", "user": 438 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDFE5_fit1_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 1.76, "p_value": 0.0, "fit_residual_plot": "SASDFE5_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFE5_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/4d7m_dimer.log", "software_version": "2.8.3", "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 TetR(D), in complex with ATc in 50 mM Tris/HCl 150 mM NaCl 10 mM MgCl2, pH 8 were collected on the EMBL P12 beam line at PETRA III (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3.1 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1.4 and 1.4 mg/ml were measured at 10°C. 20 successive 0.050 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. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 42.6, "experimental_mw_error": null, "guinier_i0_mw": 42.6, "guinier_i0_mw_error": null, "porod_mw": 48.2, "porod_mw_error": null, "pddf_i0": 7510.0, "pddf_i0_error": null, "guinier_i0": 7682.32, "guinier_i0_error": 15.74, "pddf_rg": 2.435, "pddf_rg_error": null, "guinier_rg": 2.55, "guinier_rg_error": 0.06, "pddf_dmax": 6.76, "pddf_dmax_error": null, "porod_volume": 77.16, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 14, "guinier_point_last": 172, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDFE5_datloglog_img.png", "symmetry": null, "last_modified": "2023-06-21T07:56:39.492710+02:00", "bragg_peak": [] }