{ "code": "SASDFX7", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/A", "project": { "title": "The Methionine-Rich Loop of Multicopper Oxidase McoA follows Open-To-Close Transitions with a Role in Enzyme Catalysis", "publication": { "title": "The Methionine-Rich Loop of Multicopper Oxidase McoA follows Open-To-Close Transitions with a Role in Enzyme Catalysis", "author_list": "Borges P, Brissos V, Hernandez G, Masgrau L, Lucas M, Monza E, Frazão C, Cordeiro T, Martins L", "journal": "ACS Catalysis", "doi": "10.1021/acscatal.0c01623", "pmid": null, "published_date": "2020 Jun 02" }, "status": "released", "submitted_date": "2019-06-18", "released_date": "2020-06-09" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFX7.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFX7.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFX7_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFX7_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFX7_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFX7_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFX7.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 2M", "resolution": null }, "name": "Diamond Light Source", "city": "Didcot", "country": "UK", "beamline_name": "B21", "beam_geometry": "1 x 5 mm", "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": "Aquifex aeolicus McoA metaloxidase ∆337-346", "short_name": "McoA∆337-346", "sequence": ">McoA∆337-346\r\nMLSKQSLNIPGYFLFPDGQRVSITAKWTTLEVIPGKSTDMLVYEIDNEYNPVIFLRKGQT\r\nFSADFVNNSGEDSIIHWHGFRAPWKSDGHPYYAVKDGETYSYPDFTIIDRSGTYFYHPHP\r\nHGRTGYQVYYGLAGMIIIEDEDEDNLKQALDLEYGVIDIPLIIQDKTFDSSGQLVYNPMG\r\nHMGFWGDTILVNLTPNPYMDVERKIYRFRILNGSNARPYRLALLRGNQRMRFWVIGVEGG\r\nLLDTPKEVNEILVAPGERIDILVDFRDASVNDVIKLYNFPHNLIGMGMIGMRMGNGMNMD\r\nMGMADNSEFEVMEFRVTKDSAYDKSIPQRLSEVTPINTDGAQVQRITLGMRRMVFTINGE\r\nTWEDGYANPQDINNPKVLFEQNNGDVVIIEYVNNTGMYHPMHIHGFQFQVLERSLGPLRA\r\nTDLGWKDTVIVAPMETVRIAVDMSHPYNEHQIYLLHCHILEHHDEGMMVNYRVNA", "organism": "Aquifex aeolicus", "uniprot_code": "O67206", "uniprot_range_first": 44, "uniprot_range_last": 527, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MDRRKFIKTSLFSALGFSVGGLSLLSCGGGGTTGSSSGQGSGTLSKQSLNIPGYFLFPDG\nQRVSITAKWTTLEVIPGKSTDMLVYEIDNEYNPVIFLRKGQTFSADFVNNSGEDSIIHWH\nGFRAPWKSDGHPYYAVKDGETYSYPDFTIIDRSGTYFYHPHPHGRTGYQVYYGLAGMIII\nEDEDEDNLKQALDLEYGVIDIPLIIQDKTFDSSGQLVYNPMGHMGFWGDTILVNLTPNPY\nMDVERKIYRFRILNGSNARPYRLALLRGNQRMRFWVIGVEGGLLDTPKEVNEILVAPGER\nIDILVDFRDASVNDVIKLYNFPHNLIGMGMIGMRMGMGMERGMGMGNGMNMDMGMADNSE\nFEVMEFRVTKDSAYDKSIPQRLSEVTPINTDGAQVQRITLGMRRMVFTINGETWEDGYAN\nPQDINNPKVLFEQNNGDVVIIEYVNNTGMYHPMHIHGFQFQVLERSLGPLRATDLGWKDT\nVIVAPMETVRIAVDMSHPYNEHQIYLLHCHILEHHDEGMMVNYRVNA", "mw": 54.43, "total_mw": 54.43, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50 mM Tris-HCl, 150 mM NaCl, 2 mM TCEP", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "Aquifex aeolicus McoA metaloxidase deletion mutant ∆337-346 (MCoA∆337-346)", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Oeiras, Portugal", "full_name": "Instituto de Tecnologia Química e Biológica António Xavier, Universidade de Lisboa", "webpage": "http://www.itqb.unl.pt" } ], "contributor_name": "Tiago", "contributor_surname": "Cordeiro", "orcid": "https://orcid.org/0000-0003-2663-3220" } ], "concentration_method": null, "concentration_unit": null, "date": "2017-12-04", "storage_temperature": 20.0, "cell_temperature": 20.0, "exposure_time": 3.0, "number_of_frames": 885, "wavelength": 0.0914, "sample_detector_distance": 2.69, "concentration_min": null, "concentration_max": 10.0, "sample_volume": 45.0, "flow_rate": 0.16, "s_min": 0.032, "s_max": 3.696, "total_exposure_time": null, "seccolumn": 19 }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFX7_fit1_model1_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "DAMFILT 5.0 (r9988)", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDFX7_fit1_model1.pdb", "model_mw": 41.594, "bead_radius": 2.0, "log": null, "symmetry": null, "comment": null, "user": 404 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDFX7_fit1_fixed_fit_img.png", "software": "DAMMIN", "chi_square_value": 1.118, "p_value": 0.958828, "fit_residual_plot": "SASDFX7_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFX7_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/loop18.log", "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFX7_fit2_model1_img.png", "software": "Other", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDFX7_fit2_model1.pdb", "model_mw": 54.66, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 404 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDFX7_fit2_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 1.104, "p_value": 0.794454, "fit_residual_plot": "SASDFX7_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFX7_fit2.fit", "fit_log": null, "software_version": null, "description": "" } ], "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 MCoA∆337-346 in 50 mM Tris-HCl, 150 mM NaCl, 2 mM TCEP, pH 7.5 were collected on the B21 beam line at the Diamond Light Source (Didcot, UK) using a Pilatus 2M detector at a sample-detector distance of 2.7 m and at a wavelength of λ = 0.0914 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 45.00 μl sample at 10 mg/ml was injected at a 0.16 ml/min flow rate onto a Shodex KW403 column at 20°C. 885 successive 3 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 from the sample elution peak frames.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 48.2, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 48.625, "porod_mw_error": null, "pddf_i0": 0.08495, "pddf_i0_error": null, "guinier_i0": 0.08527, "guinier_i0_error": 0.0001, "pddf_rg": 2.25, "pddf_rg_error": null, "guinier_rg": 2.286, "guinier_rg_error": 0.05, "pddf_dmax": 7.01, "pddf_dmax_error": null, "porod_volume": 77.8, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 48, "guinier_point_last": 244, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDFX7_datloglog_img.png", "symmetry": null, "last_modified": "2020-06-09T12:07:53.850745+02:00", "bragg_peak": [] }