{ "code": "SASDBP4", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/nm", "project": { "title": "Structural basis of the interaction between the putative adhesion-involved and iron-regulated FrpD and FrpC proteins of Neisseria meningitidis.", "publication": { "title": "Structural basis of the interaction between the putative adhesion-involved and iron-regulated FrpD and FrpC proteins of Neisseria meningitidis.", "author_list": "Sviridova E, Rezacova P, Bondar A, Veverka V, Novak P, Schenk G, Svergun DI, Kuta Smatanova I, Bumba L", "journal": "Sci Rep", "doi": "10.1038/srep40408", "pmid": "28084396", "published_date": "2017 Jan 13" }, "status": "released", "submitted_date": "2016-04-05", "released_date": "2017-01-26" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBP4.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBP4.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBP4_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBP4_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBP4_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBP4_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBP4.sascif", "experiment": { "instrument": { "detector": { "type": "Custom-built", "name": "Pilatus 1M-W", "resolution": 0.172 }, "name": "DORIS III, DESY", "city": "Hamburg", "country": "Germany", "beamline_name": "EMBL X33", "beam_geometry": "0.60", "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": "Iron-regulated outer membrane lipoprotein FrpD", "short_name": "FrpD", "sequence": "keqtsfnnpepmtgfehtvtfdfqgtkmvipygylarytqdnatkwlsdtpgqdaysinlieisvyykktdqgwvlepynqqnkahfiqflrdgldsvddivirkdacslsttmgerlltygvkkmpsaypeyeayedkrhipenpyfhefyyikkgenpaiithrnnrinqteedsystsvgscingftvqyypfirekqqltqqelvgyhqqveqlvqsfvnnsnkk", "organism": "Neisseria meningitidis", "uniprot_code": "Q08840", "uniprot_range_first": 43, "uniprot_range_last": 271, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MRPYATTIYQLFILFIGSVFTMTSCEPVNEKTDQKAVSAQQAKEQTSFNNPEPMTGFEHT\nVTFDFQGTKMVIPYGYLARYTQDNATKWLSDTPGQDAYSINLIEISVYYKKTDQGWVLEP\nYNQQNKAHFIQFLRDGLDSVDDIVIRKDACSLSTTMGERLLTYGVKKMPSAYPEYEAYED\nKRHIPENPYFHEFYYIKKGENPAIITHRNNRINQTEEDSYSTSVGSCINGFTVQYYPFIR\nEKQQLTQQELVGYHQQVEQLVQSFVNNSNKK", "mw": 26.756, "total_mw": 26.756, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "10 mM Tris-HCl 150 mM NaCl 0.01% NaN3", "concentration_unit": "mM", "comment": null, "additive": "150 mM NaCl, 0.01% NaN3", "concentration": 10.0, "pka": null, "ph": 7.4, "deuteration": null }, "purity_method": null, "name": "Neisseria meningitidis iron-regulated outer membrane lipoprotein FrpD", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Stanford, California, USA", "full_name": "Stanford University", "webpage": "https://www.stanford.edu/" } ], "contributor_name": "Gundolf", "contributor_surname": "Schenk", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2011-10-19", "storage_temperature": 10.0, "cell_temperature": null, "exposure_time": 15.0, "number_of_frames": 8, "wavelength": 0.15, "sample_detector_distance": 2.7, "concentration_min": null, "concentration_max": 8.4, "sample_volume": null, "flow_rate": null, "s_min": 0.085, "s_max": 6.032, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBP4_fit1_model1_img.png", "software": "DAMMIN", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDBP4_fit1_model1.pdb", "model_mw": 22.055, "bead_radius": 2.0, "log": null, "symmetry": "", "comment": "", "user": 122 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBP4_fit1_fit_img.png", "software": "DAMMIN", "chi_square_value": 1.19, "p_value": 0.000725, "fit_residual_plot": "SASDBP4_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBP4_fit1.fir", "fit_log": null, "software_version": "", "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBP4_fit2_model1_img.png", "software": "PDB (Protein Data Bank)", "pdb_link": [ { "pdb_code": "5edj", "ext_code": "5EDJ", "ext_type": "pdb", "difference_with_model": "identical" } ], "model_title": null, "type_of_model": "atomic", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDBP4_fit2_model1.pdb", "model_mw": 26.14, "bead_radius": null, "log": null, "symmetry": "", "comment": "", "user": 122 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBP4_fit2_fit_img.png", "software": "CRYSOL", "chi_square_value": 1.033, "p_value": 0.00085, "fit_residual_plot": "SASDBP4_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBP4_fit2.fit", "fit_log": null, "software_version": "", "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 from solutions of Neisseria meningitidis iron-regulated outer membrane lipoprotein FrpD in 10 mM Tris-HCl, 150 mM NaCl, 0.01% NaN3 were collected on the X33 beam line at the DORIS storage ring (DESY, Hamburg, Germany) using a Pilatus 1M-W detector (I(s) vs s; s = 4π sin θ/λ, where 2θ is the scattering angle and λ=0.15 nm). The data displayed in this entry were measured from one sample at a solute concentration of 8.4 mg/ml using an exposure time of 120 s (collected as 8 x 15 s frames). The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering from the matched solvent-blank was subtracted. The data were normalized to protein concentration.", "tags": [ "X33" ], "intensity_unit": null, "experimental_mw": 13.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 25.0, "porod_mw_error": null, "pddf_i0": 16.4, "pddf_i0_error": 0.02, "guinier_i0": 16.6, "guinier_i0_error": 0.03, "pddf_rg": 2.1, "pddf_rg_error": 0.003, "guinier_rg": 2.2, "guinier_rg_error": 0.1, "pddf_dmax": 6.5, "pddf_dmax_error": null, "porod_volume": 41.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 39, "guinier_point_last": 153, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDBP4_datloglog_img.png", "symmetry": null, "last_modified": "2023-05-25T11:21:52.654103+02:00", "bragg_peak": [] }