{ "code": "SASDBH7", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/nm", "project": { "title": "SAXS Structural Studies of Dps from Deinococcus radiodurans Highlights the Conformation of the Mobile N-Terminal Extensions.", "publication": { "title": "SAXS Structural Studies of Dps from Deinococcus radiodurans Highlights the Conformation of the Mobile N-Terminal Extensions.", "author_list": "Santos SP, Cuypers MG, Round A, Finet S, Narayanan T, Mitchell EP, Romão CV", "journal": "J Mol Biol", "doi": "10.1016/j.jmb.2017.01.008", "pmid": "28088481", "published_date": "2017 Mar 10" }, "status": "released", "submitted_date": "2016-11-04", "released_date": "2017-02-15" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBH7.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBH7.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBH7_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBH7_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBH7_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBH7_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBH7.sascif", "experiment": { "instrument": { "detector": { "type": "Dectris", "name": "Pilatus 1M", "resolution": 172.0 }, "name": "ESRF", "city": "Grenoble", "country": "France", "beamline_name": "BM29", "beam_geometry": "", "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": "N-terminal truncated DNA protection during starvation protein 1", "short_name": "Dps1t", "sequence": "HYLEEKEFQTVAETLQRNLATTISLYLKFKKYHWDIRGRFFRDLHLAYDEFIAEIFPSIDEQAERLVALG\r\nGSPLAAPADLARYSTVQVPQETVRDARTQVADLVQDLSRVGKGYRDDSQACDEANDPVTA\r\nDMYNGYAATIDKIRWMLQAIMDDERLD", "organism": "Deinococcus radiodurans R1", "uniprot_code": "Q9RS64", "uniprot_range_first": 51, "uniprot_range_last": 207, "oligomerization": "dodecamer", "molecular_type": "protein", "uniprot_sequence": "MTKKSTKSEAASKTKKSGVPETGAQGVRAGGADHADAAHLGTVNNALVNHHYLEEKEFQT\nVAETLQRNLATTISLYLKFKKYHWDIRGRFFRDLHLAYDEFIAEIFPSIDEQAERLVALG\nGSPLAAPADLARYSTVQVPQETVRDARTQVADLVQDLSRVGKGYRDDSQACDEANDPVTA\nDMYNGYAATIDKIRWMLQAIMDDERLD", "mw": 18.037, "total_mw": 216.444, "number_molecules": 12, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM Tris-HCl, 150 mM NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "Dps1 truncated, DNA binding protein under starvation conditions (SEC-SAXS)", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Oeiras, Portugal", "full_name": "Instituto de Tecnologia Química e Biológica António Xavier, Universidade de Lisboa", "webpage": "http://www.itqb.unl.pt" } ], "contributor_name": "Sandra", "contributor_surname": "Santos", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2013-11-22", "storage_temperature": 20.0, "cell_temperature": 20.0, "exposure_time": 1.0, "number_of_frames": 1500, "wavelength": 0.09919, "sample_detector_distance": 2.81, "concentration_min": null, "concentration_max": 10.0, "sample_volume": null, "flow_rate": null, "s_min": 0.063, "s_max": 4.485, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBH7_fit1_model1_img.png", "software": "GASBOR", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "2.2i", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDBH7_fit1_model1.pdb", "model_mw": null, "bead_radius": 1.9, "log": null, "symmetry": "P23", "comment": "", "user": 162 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBH7_fit1_fit_img.png", "software": null, "chi_square_value": 10.6, "p_value": 0.0, "fit_residual_plot": "SASDBH7_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBH7_fit1.fir", "fit_log": null, "software_version": null, "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": null, "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data, I(s) vs s (s = 4π sin θ/λ, where 2θ is the scattering angle) were collected from a sample of truncated Dps1, (DNA binding protein under starvation conditions) using continuous-flow size-exclusion chromatography SAXS (SEC-SAXS) at the BM29 beam line on the ESRF storage ring (Grenoble, France). Data (1500 successive 1 second frames), were collected using a Pilatus 1M detector at a sample-detector distance of 2.8 m and at a wavelength of λ = 0.09919 nm. The SEC mobile phase consisted of 20 mM Tris-HCl, 150 mM NaCl, pH 7.5, (20°C) with a sample injection concentration of 10 mg/ml. Data obtained from solute-free eluates and SEC-elution peak were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted from the SEC-peak frames to produce the data displayed in this entry.", "tags": [], "intensity_unit": null, "experimental_mw": 171.15, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 171.16, "porod_mw_error": null, "pddf_i0": 52.14, "pddf_i0_error": 0.04, "guinier_i0": 52.35, "guinier_i0_error": 0.048, "pddf_rg": 3.83, "pddf_rg_error": 0.003, "guinier_rg": 3.88, "guinier_rg_error": 0.01, "pddf_dmax": 9.99, "pddf_dmax_error": null, "porod_volume": 290.96, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 60, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDBH7_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }