The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
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{
"code": "SASDWK4",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Extremophilic hemoglobins: The structure of Shewanella benthica truncated hemoglobin N",
"publication": {
"title": "Extremophilic hemoglobins: The structure of Shewanella benthica truncated hemoglobin N",
"author_list": "Martinez Grundman J, Schultz T, Schlessman J, Johnson E, Gillilan R, Lecomte J",
"journal": "Journal of Biological Chemistry",
"doi": "10.1016/j.jbc.2025.108223",
"pmid": null,
"published_date": "2025 Jan"
},
"status": "released",
"submitted_date": "2025-01-09",
"released_date": "2025-01-30"
},
"pddf_data": null,
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDWK4.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWK4_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWK4_kratky_img.png",
"pddf_plot": null,
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWK4_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDWK4.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Eiger 4M",
"resolution": 75.0
},
"name": "Cornell High Energy Synchrotron Source (CHESS)",
"city": "Ithaca, NY",
"country": "USA",
"beamline_name": "ID7A1 BioSAXS / HP-Bio Beamline",
"beam_geometry": null,
"type_of_source": "X-ray synchrotron",
"point_source": true,
"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": "Group 1 truncated hemoglobin (C51S, C71S)",
"short_name": "S2SbHbN",
"sequence": "SLYERLGGEQKIARIAADIFDTHATNPTVASRYKDSDRERVIKMVTEFLSAGTGGPQDY\r\nTGKSMPEAHRSMNINEAEYLAVIDDIMVALDKNEVGDQEKQELLMIAYSLKGEIIGA",
"organism": "Shewanella benthica KT99",
"uniprot_code": "A9DF82",
"uniprot_range_first": 2,
"uniprot_range_last": 117,
"oligomerization": "other",
"molecular_type": "protein",
"uniprot_sequence": "MSLYERLGGEQKIARIAADIFDTHATNPTVASRYKDSDRERVIKMVTEFLCAGTGGPQDY\nTGKSMPEAHRCMNINEAEYLAVIDDIMVALDKNEVGDQEKQELLMIAYSLKGEIIGA",
"mw": 12.823,
"total_mw": 12.823,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "Shewanella benthica truncated hemoglobin N, S2SbHbN - UniProt A9DF82- with Met cleaved N-terminus and C51S, C71S point mutations."
}
],
"buffer": {
"name": "14 mM Tris, 6 mM potassium phosphate",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.0,
"deuteration": null
},
"purity_method": null,
"name": "Shewanella benthica hemoglobin",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Ithaca, NY, United States",
"full_name": "Cornell University",
"webpage": "https://www.cornell.edu/"
}
],
"contributor_name": "Richard",
"contributor_surname": "Gillilan",
"orcid": ""
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2022-05-01",
"storage_temperature": 4.0,
"cell_temperature": 23.0,
"exposure_time": 2.0,
"number_of_frames": 1,
"wavelength": 0.1241,
"sample_detector_distance": 1.648,
"concentration_min": null,
"concentration_max": 10.0,
"sample_volume": 100.0,
"flow_rate": 0.5,
"s_min": 0.086,
"s_max": 4.66,
"total_exposure_time": null,
"seccolumn": 1
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDWK4_fit1_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "7tt9",
"ext_code": "7TT9",
"ext_type": "pdb",
"difference_with_model": "identical"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDWK4_fit1_model1.pdb",
"model_mw": 13.42,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "PDB 7TT9 monomer",
"user": 9
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDWK4_fit1_model2_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "7tt9",
"ext_code": "7TT9",
"ext_type": "pdb",
"difference_with_model": "identical"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDWK4_fit1_model2.pdb",
"model_mw": 26.83,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "PDB 7TT9 dimer",
"user": 9
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWK4_fit1_fixed_fit_img.png",
"software": "OLIGOMER",
"chi_square_value": 1.01,
"p_value": 0.0122,
"fit_residual_plot": "SASDWK4_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDWK4_fit1.fit",
"fit_log": null,
"software_version": "7.1",
"description": "*** O L I G O M E R *** \r\n================================================================================\r\n 04-Jan-2025 08:20:45\r\n Option 0: a set of form-factors and several sets of experimental data \r\n Form-factor file mon_dimer.dat\r\n Real oligomer weights 1618 3236 10235\r\n Oligomer radii of gyration 13.97 19.74 0.00\r\n Experimental data file S_heme_beth_1_data_000703.dat Range of Scattering angle: 0.01 0.20\r\n Using non-negativity condition \r\n Using constant as additional component \r\n Output file S_heme_beth_1_data_000703.fit\r\n Chi^2 <MW> <Rg> Volume fractions +- errors\r\n--------------------------------------------------------------------------------\r\n================================================================================\r\nS_heme_beth_1_data_0 1.01 2578. 18.4 0.407+-0.013 0.593+-0.009 0.00000E+00+- 0.00000E+00\r\n================================================================================"
}
],
"estimated_volume_method": null,
"pddf_software": null,
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": "40% monomer + 60% dimer. Single 2-sec exposure from peak of SAXS chromatogram. Fit to monomer and dimer from PDB: 7TT9 via OLIGOMER.",
"experiment_description": null,
"tags": [],
"intensity_unit": "1/cm",
"experimental_mw": 18.2,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": null,
"pddf_i0_error": null,
"guinier_i0": 0.0177494,
"guinier_i0_error": null,
"pddf_rg": null,
"pddf_rg_error": null,
"guinier_rg": 1.755,
"guinier_rg_error": 0.02,
"pddf_dmax": 5.8,
"pddf_dmax_error": null,
"porod_volume": 30.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 28,
"guinier_point_last": 297,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDWK4_datloglog_img.png",
"symmetry": null,
"last_modified": "2025-01-30T16:04:48.773317+01:00",
"bragg_peak": []
}
