{ "code": "SASDEM3", "status": "Published", "type_of_curve": "Merged", "angular_unit": "1/nm", "project": { "title": "The biological assembly of OXA-48 reveals a dimer interface with high charge complementarity and very high affinity.", "publication": { "title": "The biological assembly of OXA-48 reveals a dimer interface with high charge complementarity and very high affinity.", "author_list": "Lund BA, Thomassen AM, Nesheim BHB, Carlsen TJO, Isaksson J, Christopeit T, Leiros HS", "journal": "FEBS J", "doi": "10.1111/febs.14643", "pmid": "30153368", "published_date": "2018 Aug 28" }, "status": "released", "submitted_date": "2018-08-30", "released_date": "2018-08-31" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEM3.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEM3.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEM3_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEM3_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEM3_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEM3_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEM3.sascif", "experiment": { "instrument": { "detector": { "type": "Dectris", "name": "Pilatus 1M", "resolution": 172.0 }, "name": "ESRF", "city": "Grenoble", "country": "France", "beamline_name": "BM29", "beam_geometry": "", "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": "Beta-lactamase", "short_name": "OXA-48", "sequence": "AKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALD\r\nLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAF\r\nDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGD\r\nYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEK\r\nIIP", "organism": "Klebsiella pneumoniae", "uniprot_code": "Q6XEC0", "uniprot_range_first": 22, "uniprot_range_last": 265, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLK\nRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVV\nPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNK\nLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMD\nMPTSDGLGLRQAITKEVLKQEKIIP", "mw": 28.218, "total_mw": 56.436, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50 mM HEPES 50 mM K2SO4", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.0, "deuteration": null }, "purity_method": null, "name": "Dimeric class D beta-lactamase OXA-48", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "UiT", "address": "Tromso, Norway", "full_name": "UiT - The Arctic University of Norway", "webpage": "https://en.uit.no/" } ], "contributor_name": "Bjarte Aarmo", "contributor_surname": "Lund", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2017-02-23", "storage_temperature": 25.0, "cell_temperature": 25.0, "exposure_time": 10.0, "number_of_frames": 10, "wavelength": 0.09919, "sample_detector_distance": 2.867, "concentration_min": 0.1, "concentration_max": 13.0, "sample_volume": null, "flow_rate": null, "s_min": 0.079, "s_max": 4.899, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEM3_fit1_model1_img.png", "software": "PDB (Protein Data Bank)", "pdb_link": [ { "pdb_code": "5dtk", "ext_code": "5DTK", "ext_type": "pdb", "difference_with_model": "derived" } ], "model_title": null, "type_of_model": "atomic", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEM3_fit1_model1.pdb", "model_mw": 57.14, "bead_radius": 1.9, "log": null, "symmetry": "", "comment": "chains A and D", "user": 230 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/5dtk-A-D00_fit_img.png", "software": "CRYSOL", "chi_square_value": 5.025, "p_value": 0.0, "fit_residual_plot": "5dtk-A-D00_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEM3_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/5dtk-A-D00.log", "software_version": "28", "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of dimeric class D beta-lactamase (OXA-48) in 50 mM HEPES, 50 mM K2SO4, pH 7, were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Dectris Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.09919 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.1 and 13 mg/ml were measured at 25°C. 10 successive 10 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. The low angle data collected at lower concentration(s) were merged with the higher concentration high angle data to yield the final composite scattering curve.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 50.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 46.0, "porod_mw_error": null, "pddf_i0": 26.79, "pddf_i0_error": null, "guinier_i0": 27.04, "guinier_i0_error": 0.052, "pddf_rg": 2.476, "pddf_rg_error": null, "guinier_rg": 2.47, "guinier_rg_error": 0.018, "pddf_dmax": 7.35, "pddf_dmax_error": null, "porod_volume": 74.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 2, "guinier_point_last": 96, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDEM3_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }