{ "code": "SASDV54", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/nm", "project": { "title": "Structural-function relationship of YdaS, a Cro-type repressor in the cryptic prophage CP-933P from Escherichia coli O157:H7", "publication": null, "status": "released", "submitted_date": "2024-07-01", "released_date": "2024-07-30" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDV54.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDV54.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDV54_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDV54_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDV54_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDV54_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDV54.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus3 2M", "resolution": 0.172 }, "name": "ESRF", "city": "Grenoble", "country": "France", "beamline_name": "BM29", "beam_geometry": "point", "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": "Phage antirepressor protein Cro", "short_name": "YdaS protein", "sequence": "MTLKEFIKSLRVGDAKKFAARLGVSPSYLSQMASGRTAISPTRALMIESATEGQVSRAELRPHDWELIWPEYASGIRLGQTHVVHAEGDCSACLSDGVDSGSSHHHHHH", "organism": "Escherichia coli O157:H7", "uniprot_code": "Q8XAD7", "uniprot_range_first": 1, "uniprot_range_last": 100, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MTLKEFIKSLRVGDAKKFAARLGVSPSYLSQMASGRTAISPTRALMIESATEGQVSRAEL\nRPHDWELIWPEYASGIRLGQTHVVHAEGDCSACLSDGVDS", "mw": 11.902, "total_mw": 23.804, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "Phage antirepressor protein Cro. The protein construct used for SAXS contains an additional non-native polyhistidine tag at the C-terminus (GSSHHHHHH)." }, { "long_name": "IR1 22 base pair dsDNA", "short_name": "IR1", "sequence": "TTGTTTAGTGATTACTAAAGAT\r\nAACAAATCACTAATGATTTCTA", "organism": null, "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "DNA", "uniprot_sequence": "", "mw": 13.606, "total_mw": 13.606, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "" } ], "buffer": { "name": "20 mM sodium acetate, 150 mM NaCl, 1 mM TCEP", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 5.5, "deuteration": null }, "purity_method": null, "name": "YdaS, a cro-type repressor from Escherichai coli O157:H7 cryptic prophage CP-933 bound to a 22 base pair dsDNA.", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "VUB", "address": "Pleinlaan 2 1050 Brussel ", "full_name": "Vrije Universiteit Brussel", "webpage": "http://www.vub.ac.be/" } ], "contributor_name": "Marusa", "contributor_surname": "Prolic Kalinsek", "orcid": "https://orcid.org/0000-0003-4175-1858" } ], "concentration_method": null, "concentration_unit": null, "date": "2021-04-13", "storage_temperature": null, "cell_temperature": 15.0, "exposure_time": null, "number_of_frames": null, "wavelength": 0.0992, "sample_detector_distance": 2.81, "concentration_min": null, "concentration_max": 15.0, "sample_volume": 45.0, "flow_rate": 0.16, "s_min": 0.044, "s_max": 5.205, "total_exposure_time": null, "seccolumn": 34 }, "fits": [ { "models": [ { "model_plot": null, "software": "Other [static image]", "pdb_link": [], "model_title": null, "type_of_model": "other", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDV54_fit1_model1.png", "model_mw": null, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 9 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDV54_fit1_fixed_fit_img.png", "software": "Other", "chi_square_value": 1.2621, "p_value": 0.0148, "fit_residual_plot": "SASDV54_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDV54_fit1.saxs", "fit_log": null, "software_version": "calcSAXS", "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": "The atomic coordinates of the full model ensemble are made available in the full entry zip archive. X-ray exposure time = UNKNOWN. Number of sample data frames = UNKNOWN.", "experiment_description": "Synchrotron SAXS data from solutions of YdaS, a cro-type repressor from Escherichai coli O157:H7 cryptic prophage CP-933 bound to a 22 base pair dsDNA in 20 mM sodium acetate, 150 mM NaCl, 1 mM TCEP, pH 5.5 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus3 2M detector at a sample-detector distance of 2.8 m and at a wavelength of λ = 0.0992 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 45.00 μl sample at 15 mg/ml was injected at a 0.16 ml/min flow rate onto a Agilent AdvanceBio SEC 300Å, 4.6 x 150 mm column at 15°C. 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": 35.4, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 140.7, "pddf_i0_error": null, "guinier_i0": 140.401, "guinier_i0_error": null, "pddf_rg": 2.898, "pddf_rg_error": null, "guinier_rg": 2.84, "guinier_rg_error": 0.009, "pddf_dmax": 10.12, "pddf_dmax_error": null, "porod_volume": 52.95, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 21, "guinier_point_last": 76, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDV54_datloglog_img.png", "symmetry": null, "last_modified": "2024-07-30T18:06:40.919061+02:00", "bragg_peak": [] }