{ "code": "SASDUX9", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/nm", "project": { "title": "A genetically encoded anomalous SAXS ruler to probe the dimensions of intrinsically disordered proteins.", "publication": { "title": "A genetically encoded anomalous SAXS ruler to probe the dimensions of intrinsically disordered proteins.", "author_list": "Yu M, Gruzinov AY, Ruan H, Scheidt T, Chowdhury A, Giofrè S, Mohammed ASA, Caria J, Sauter PF, Svergun DI, Lemke EA", "journal": "Proc Natl Acad Sci U S A", "doi": "10.1073/pnas.2415220121", "pmid": "39642200", "published_date": "2024 Dec 10" }, "status": "released", "submitted_date": "2024-06-05", "released_date": "2024-12-09" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDUX9.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDUX9.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUX9_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUX9_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDUX9_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUX9_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDUX9.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 6M", "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": "Elastin-like polypeptide labeled with unnatural amino acid diBrK", "short_name": "Br-labeled ELP", "sequence": "SSGGVGVPGGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVGWPSGA", "organism": "synthetic construct", "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "", "mw": 12.893, "total_mw": 12.893, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "Br-labelled elastin-like polypeptide incorporating the unnatural amino acid diBrK (N-ε-3,5-dibromobenzyloxycarbonyl-L-lysine). The positions of the diBrK (*) in the protein sequence are:\r\n\r\nSSGGVGVPG*GVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGV\r\nGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGV\r\nGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGV\r\nGV*GWPSGA" } ], "buffer": { "name": "phosphate buffered saline containing 6 M urea, 0.3 M KCl, 5 mM DTT", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.4, "deuteration": null }, "purity_method": null, "name": "Br-labelled Elastin-like Polypeptide (ELP) in 6 M Urea", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "DESY", "address": null, "full_name": "Beamline P11 (PETRA III), Deutsches Elektronen-Synchrotron", "webpage": null } ], "contributor_name": "Andrey", "contributor_surname": "Gruzinov", "orcid": "https://orcid.org/0000-0001-8598-5491" } ], "concentration_method": null, "concentration_unit": null, "date": "2023-07-02", "storage_temperature": 10.0, "cell_temperature": 20.0, "exposure_time": 0.25, "number_of_frames": 2400, "wavelength": 0.092, "sample_detector_distance": 3.1, "concentration_min": null, "concentration_max": 20.0, "sample_volume": 80.0, "flow_rate": 0.25, "s_min": 0.062, "s_max": 4.432, "total_exposure_time": null, "seccolumn": 4 }, "fits": [], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": "Br-labeled ELP in 6 M urea measured at 13428 eV. SAXS data measured at several different energies spanning the K-absorbtion edge of bromine are made available in the full entry zip archive.", "experiment_description": "Synchrotron SAXS data from solutions of Br-labelled ELP in phosphate buffered saline containing 6 M urea, 0.3 M KCl, 5 mM DTT, pH 7.4 were collected on the EMBL P12 beam line at PETRA III (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3.1 m and at a wavelength of λ = 0.092 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 80.00 μl sample at 20 mg/ml was injected at a 0.25 ml/min flow rate onto a GE Superdex 75 Increase 5/150 column at 20°C. 2400 successive 0.250 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.", "tags": [ "idp" ], "intensity_unit": "1/cm", "experimental_mw": 13.2, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 37.0, "porod_mw_error": null, "pddf_i0": 0.009773, "pddf_i0_error": null, "guinier_i0": 0.00953452, "guinier_i0_error": null, "pddf_rg": 4.141, "pddf_rg_error": null, "guinier_rg": 3.76, "guinier_rg_error": 0.037, "pddf_dmax": 18.08, "pddf_dmax_error": null, "porod_volume": 47.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 6, "guinier_point_last": 50, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDUX9_datloglog_img.png", "symmetry": null, "last_modified": "2024-12-09T12:10:06.285128+01:00", "bragg_peak": [] }