{ "code": "SASDVA8", "status": "Published", "type_of_curve": "Merged", "angular_unit": "1/A", "project": { "title": "SidF, a dual substrate N5-acetyl-N5-hydroxy-L-ornithine transacetylase involved in Aspergillus fumigatus siderophore biosynthesis", "publication": { "title": "SidF, a dual substrate N5-acetyl-N5-hydroxy-L-ornithine transacetylase involved in Aspergillus fumigatus siderophore biosynthesis", "author_list": "Poonsiri T, Stransky J, Demitri N, Haas H, Cianci M, Benini S", "journal": "Journal of Structural Biology: X", "doi": "10.1016/j.yjsbx.2024.100119", "pmid": null, "published_date": "2025 Jun" }, "status": "released", "submitted_date": "2024-10-21", "released_date": "2025-01-02" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDVA8.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVA8.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVA8_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVA8_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVA8_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVA8_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVA8.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Eiger R 1M", "resolution": 0.75 }, "name": "Institute of Biotechnology, Czech Academy of Sciences/Centre of Molecular Structure", "city": "Vestec", "country": "Czech Republic", "beamline_name": "Anton Paar SAXSpoint 2.0", "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": "N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF", "short_name": "SidF N-ter", "sequence": "MGSSHHHHHHSSGENLYFQGHMATQSSTELPQINMTTAEPTSANKRTYPWVKLPHPYLTSYAIHVVSESTPRVLQLRLHDDQKGQALPEPLHSASLTYTDIAFDEAAQEIPDNDNSPWARSRRAPGTSFHWTGQEPPTLGQIWNVIHALFLTYPQHEIVRLDLNGSGKDIIREECLRTGLAVPFPSPRVPFGTENRPSETDTLILLRSAFWQGAGSPVGPR", "organism": "Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)", "uniprot_code": "Q4WF55", "uniprot_range_first": 1, "uniprot_range_last": 200, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MATQSSTELPQINMTTAEPTSANKRTYPWVKLPHPYLTSYAIHVVSESTPRVLQLRLHDD\nQKGQALPEPLHSASLTYTDIAFDEAAQEIPDNDNSPWARSRRAPGTSFHWTGQEPPTLGQ\nIWNVIHALFLTYPQHEIVRLDLNGSGKDIIREECLRTGLAVPFPSPRVPFGTENRPSETD\nTLILLRSAFWQGAGSPVGPRPIWAVDHGIHGLLRRSGSSYPPLAQNYEFSMKFPSERIYT\nRHPIRPQKPAPGSLVYSRYIPHLDQHFSLMVVDWQNEEHLQLFHKWQNDPRVAKGWNETG\nDLEHHRNYLRQLHEDKHVLCLFGRFDDFPFSYFEVYWAKEDHYGAHYDAGDYDRGRHSLV\nGESSVRGAYRVNAWWSSLIHYIFLDEPRTMCVVGEPKATNTTVLSYENAHGLTVQKYVDL\nGHKRSVHVYCSREKWFQLCPLFWDGRERPLESSDRMAWDAKL", "mw": 24.707, "total_mw": 24.707, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "The protein construct used for SAXS contains a non-native polyhistidine tag, with additional non-native amino acids at the N-terminus (MGSSHHHHHHSSGENLYFQGH)." } ], "buffer": { "name": "50 mM Tris, 200 mM NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "The N-terminal domain of N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Thailand", "full_name": "Mahidol University", "webpage": "https://mahidol.ac.th/" } ], "contributor_name": "Thanalai", "contributor_surname": "Poonsiri", "orcid": "" } ], "concentration_method": null, "concentration_unit": null, "date": "2023-01-18", "storage_temperature": 20.0, "cell_temperature": 20.0, "exposure_time": 15.0, "number_of_frames": 60, "wavelength": 0.134, "sample_detector_distance": 0.571, "concentration_min": 5.0, "concentration_max": 5.0, "sample_volume": 400.0, "flow_rate": 0.05, "s_min": 0.141, "s_max": 3.045, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVA8_fit1_model1_img.png", "software": "EOM/RANCH", "pdb_link": [], "model_title": null, "type_of_model": "mix", "software_version": "2", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDVA8_fit1_model1.pdb", "model_mw": 24.26, "bead_radius": 1.9, "log": null, "symmetry": null, "comment": null, "user": 1131 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVA8_fit1_model2_img.png", "software": "EOM/RANCH", "pdb_link": [], "model_title": null, "type_of_model": "mix", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDVA8_fit1_model2.pdb", "model_mw": 24.26, "bead_radius": 1.9, "log": null, "symmetry": null, "comment": null, "user": 1131 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVA8_fit1_model3_img.png", "software": "EOM/RANCH", "pdb_link": [], "model_title": null, "type_of_model": "mix", "software_version": "2", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDVA8_fit1_model3.pdb", "model_mw": 24.26, "bead_radius": 1.9, "log": null, "symmetry": null, "comment": null, "user": 1131 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVA8_fit1_fixed_fit_img.png", "software": "EOM/GAJOE", "chi_square_value": 1.168, "p_value": 0.0464, "fit_residual_plot": "SASDVA8_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVA8_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/logFile_002_1_mTptFGn.log", "software_version": "2", "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 sidF N-terminal domain in 50 mM Tris, 200 mM NaCl, pH 8 were collected using an Anton Paar SAXSpoint 2.0 instrument at the Institute of Biotechnology, Czech Academy of Sciences/Centre of Molecular Structure (Vestec, Czech Republic) equipped with an Eiger R 1M detector at a sample-detector distance of 0.6 m and at a wavelength of λ = 0.134 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). A sample concentration at 5 mg/ml was measured at 20°C. 60 successive 15 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": [], "intensity_unit": "arbitrary", "experimental_mw": 23.1, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 18.7, "porod_mw_error": null, "pddf_i0": 0.04151, "pddf_i0_error": null, "guinier_i0": 0.0407958, "guinier_i0_error": null, "pddf_rg": 2.32, "pddf_rg_error": null, "guinier_rg": 2.185, "guinier_rg_error": 1.728, "pddf_dmax": 8.9, "pddf_dmax_error": null, "porod_volume": 29.9, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 4, "guinier_point_last": 40, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDVA8_datloglog_img.png", "symmetry": null, "last_modified": "2025-01-02T12:10:48.691893+01:00", "bragg_peak": [] }