{ "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 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": [] }