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{
"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": []
}
