{ "code": "SASDFS4", "status": "Published", "type_of_curve": "Extrapolated to infinite dilution", "angular_unit": "1/A", "project": { "title": "Construction of a Quadrangular Tetramer and a Cage-Like Hexamer from Three-Helix Bundle-Linked Fusion Proteins.", "publication": { "title": "Construction of a Quadrangular Tetramer and a Cage-Like Hexamer from Three-Helix Bundle-Linked Fusion Proteins.", "author_list": "Miyamoto T, Hayashi Y, Yoshida K, Watanabe H, Uchihashi T, Yonezawa K, Shimizu N, Kamikubo H, Hirota S", "journal": "ACS Synth Biol", "doi": "10.1021/acssynbio.9b00019", "pmid": "30966743", "published_date": "2019 Apr 16" }, "status": "released", "submitted_date": "2019-03-28", "released_date": "2019-04-24" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFS4.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFS4.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFS4_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFS4_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFS4_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFS4_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFS4.sascif", "experiment": { "instrument": { "detector": { "type": "Pilatus", "name": "Pilatus 200K", "resolution": 172.0 }, "name": "Nara Institute of Science and Technology", "city": "Ikoma", "country": "Japan", "beamline_name": "Rigaku Nano-Viewer", "beam_geometry": null, "type_of_source": "X-ray in house", "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": "HP0242 from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain", "short_name": "Fusion protein2", "sequence": "MGSSHHHHHHSSGLVPRGSHMRDYSELEIFEGNPLDKWNDIIFHASKKASKKELERLLELLALCETFIEKEDLEEKFESFAKALRIDEELQQKIESRKTDIVIQSMANILSALFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSAILASPNPDEKTKEELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQHSTLSRKFVEVMSEYNATQSDYGSGGEIAAIKQEIAAIKKEIAAIKWEIAAIKQGYG", "organism": "Helicobacter pylori, Rattus norvegicus, de novo design", "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "hexamer", "molecular_type": "protein", "uniprot_sequence": null, "mw": 29.855, "total_mw": 179.13, "number_molecules": 6, "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": 8.0, "deuteration": null }, "purity_method": null, "name": "HP0242 from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain (Domain A (PDB:3MLI)-Linker (PDB:1BR0)-Domain B (PDB:4DZL))", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Japan", "full_name": "Nara Institute of Science and Technology", "webpage": "http://www.naist.jp/en/" } ], "contributor_name": "Hironari", "contributor_surname": "Kamikubo", "orcid": "https://orcid.org/0000-0002-0878-6488" } ], "concentration_method": null, "concentration_unit": null, "date": "2017-03-29", "storage_temperature": 4.0, "cell_temperature": 20.0, "exposure_time": 60.0, "number_of_frames": 25, "wavelength": 0.15418, "sample_detector_distance": 0.75, "concentration_min": 1.9, "concentration_max": 6.8, "sample_volume": null, "flow_rate": null, "s_min": 0.138, "s_max": 3.003, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFS4_fit1_model1_img.png", "software": "CORAL", "pdb_link": [ { "pdb_code": "3mli", "ext_code": "3MLI", "ext_type": "pdb", "difference_with_model": "derived" }, { "pdb_code": "1br0", "ext_code": "1BR0", "ext_type": "pdb", "difference_with_model": "derived" }, { "pdb_code": "4dzl", "ext_code": "4DZL", "ext_type": "pdb", "difference_with_model": "derived" } ], "model_title": null, "type_of_model": "mix", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDFS4_fit1_model1.pdb", "model_mw": 180.1, "bead_radius": 1.9, "log": "https://www.sasbdb.org/media/log_files/hex402.log", "symmetry": null, "comment": null, "user": 432 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/hex402-1_fixed_fit_img.png", "software": "CORAL", "chi_square_value": 0.1, "p_value": 8.8e-05, "fit_residual_plot": "hex402-1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFS4_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/hex402.log", "software_version": "5", "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": null, "experiment_description": "SAXS data from solutions of the fusion protein2 in 20 mM Tris-HCl, 150 mM KCl, pH 8.0 were collected using a Nano-Viewer (Rigaku, Japan) at NAIST (Nara, Japan) equipped with a Pilatus 200K detector at a sample-detector distance of 0.75 m and at a wavelength of λ = 0.15418 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Twenty-five successive 60 second frames were collected at a sample temperature of 20°C. Solute concentrations ranging between 1.9 and 6.8 mg/ml were measured. The data were normalized to the intensity of the direct beam and radially averaged. The scattering from the solvent-blank was subtracted. The scattering profile in this entry represents an extrapolation to infinite dilution.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 187.0, "experimental_mw_error": null, "guinier_i0_mw": 187.0, "guinier_i0_mw_error": 10.0, "porod_mw": 401.0, "porod_mw_error": null, "pddf_i0": 40.9, "pddf_i0_error": 2.2, "guinier_i0": 40.11, "guinier_i0_error": 3.11, "pddf_rg": 7.0, "pddf_rg_error": 0.3, "guinier_rg": 6.53, "guinier_rg_error": 0.6, "pddf_dmax": 24.0, "pddf_dmax_error": null, "porod_volume": 642.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 8, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDFS4_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }