{ "code": "SASDVG6", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/A", "project": { "title": "Structural insights into the enzymatic breakdown of azomycin-derived antibiotics by 2-nitroimdazole hydrolase (NnhA).", "publication": { "title": "Structural insights into the enzymatic breakdown of azomycin-derived antibiotics by 2-nitroimdazole hydrolase (NnhA).", "author_list": "Ahmed FH, Liu JW, Royan S, Warden AC, Esquirol L, Pandey G, Newman J, Scott C, Peat TS", "journal": "Commun Biol", "doi": "10.1038/s42003-024-07336-6", "pmid": "39702827", "published_date": "2024 Dec 19" }, "status": "released", "submitted_date": "2024-08-26", "released_date": "2024-12-23" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDVG6.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVG6.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVG6_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVG6_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVG6_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVG6_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVG6.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus3 X 2M", "resolution": 172.0 }, "name": "Australian Synchrotron", "city": "Melbourne", "country": "Australia", "beamline_name": "BioSAXS", "beam_geometry": null, "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": "2-nitroimidazole nitrohydrolase (T2I, G14D, K73R)", "short_name": "NnhA", "sequence": "MHHHHHHMITVDKRPSSRGYDDWRLSDIPQYKDGISTYEFVRATHEADYRTHQAEPVAGRTFGFNGIGRLTEVALHMPTRYTLHDQSSQYKESPSFFQGLMGVPDRGPVDLAAFQRETEELATAFENNGIKVHWVDYPEEPANPYGPLMGHVFLSWGSIWRGGSVISRFGFLPGMVGVSEYLAKWAWNTLNIPPLVAITEGAMEPGACNMIADEVLVTCLSASYDQRGTDQLVAAISKTSGTEEFHNLQLRPAVEGFFNKATGACAhPdININAIDVGKLVVSPAALDWDARTWLYDNNFELIEADPDEQREFLAPCnVLLLEPGKVIAHADCHKTNQKIRDAGVEVIEVTGTEIRKAcGGIKcRVMQINREPGPTLADVRNRVWR", "organism": "Mycobacterium sp. (strain JS330)", "uniprot_code": "F4ZCI3", "uniprot_range_first": 1, "uniprot_range_last": 379, "oligomerization": "hexamer", "molecular_type": "protein", "uniprot_sequence": "MTTVDKRPSSRGYGDWRLSDIPQYKDGISTYEFVRATHEADYRTHQAEPVAGRTFGFNGI\nGRLTEVALHMPTKYTLHDQSSQYKESPSFFQGLMGVPDRGPVDLAAFQRETEELATAFEN\nNGIKVHWVDYPEEPANPYGPLMGHVFLSWGSIWRGGSVISRFGFLPGMVGVSEYLAKWAW\nNTLNIPPLVAITEGAMEPGACNMIADEVLVTCLSASYDQRGTDQLVAAISKTSGTEEFHN\nLQLRPAVEGFFNKATGACAHPDININAIDVGKLVVSPAALDWDARTWLYDNNFELIEADP\nDEQREFLAPCNVLLLEPGKVIAHADCHKTNQKIRDAGVEVIEVTGTEIRKACGGIKCRVM\nQINREPGPTLADVRNRVWR", "mw": 43.08, "total_mw": 258.48, "number_molecules": 6, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "Soluble NnhA from Mycobacterium sp. JS330 (carrying the point mutations T2I, G14D K73R). The protein construct used for SAXS contains an additional non-native N-terminal polyhistidine tag (MHHHHHH)." } ], "buffer": { "name": "25 mM Tris-HCl, 150 mM NaCl, 5% (v/v) glycerol", "concentration_unit": null, "comment": "TBS+G", "additive": null, "concentration": null, "pka": null, "ph": 7.6, "deuteration": null }, "purity_method": null, "name": "2-nitroimidazole nitrohydrolase", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Aarhus, Denmark", "full_name": "Aarhus University", "webpage": "http://www.au.dk" } ], "contributor_name": "Santana", "contributor_surname": "Royan", "orcid": "https://orcid.org/0000-0002-2312-3463" } ], "concentration_method": null, "concentration_unit": null, "date": "2024-08-06", "storage_temperature": 25.0, "cell_temperature": 25.0, "exposure_time": 1.0, "number_of_frames": 29, "wavelength": 0.1, "sample_detector_distance": 3.151, "concentration_min": null, "concentration_max": 3.5, "sample_volume": 50.0, "flow_rate": 0.4, "s_min": 0.068, "s_max": 3.998, "total_exposure_time": null, "seccolumn": 29 }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVG6_fit1_model1_img.png", "software": "REFMAC", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDVG6_fit1_model1.pdb", "model_mw": 246.5, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 1112 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVG6_fit1_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 2.404, "p_value": 0.0, "fit_residual_plot": "SASDVG6_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVG6_fit1.fit", "fit_log": null, "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVG6_fit2_model1_img.png", "software": "DAMFILT", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDVG6_fit2_model1.pdb", "model_mw": null, "bead_radius": null, "log": "https://www.sasbdb.org/media/log_files/refine_A_S_ZB_Nnh035_S200_e3cb87d9_E1.log", "symmetry": null, "comment": null, "user": 1112 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVG6_fit2_fixed_fit_img.png", "software": "DAMMIN", "chi_square_value": 1.62, "p_value": 0.5596, "fit_residual_plot": "SASDVG6_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVG6_fit2.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/refine_A_S_ZB_Nnh035_S200_e3cb87d9_E1_VBIdNNK.log", "software_version": null, "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": "The molecular weight estimate (243 kDa) was calculated from Bayesian Inference (84.5% probability) in the molecular weight range credibility interval spanning 221.1 kDa to 372.7 kDa (98.7% probability).", "experiment_description": "Synchrotron SAXS data from solutions of 2-nitroimidazole nitrohydrolase in 25 mM Tris-HCl, 150 mM NaCl, 5% (v/v) glycerol, pH 7.6 were collected on the BioSAXS beam line at the Australian Synchrotron (Melbourne, Australia) using a Pilatus 2M detector at a sample-detector distance of 3.2 m and at a wavelength of λ = 0.1 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 50.00 μl sample at 3.5 mg/ml was injected at a 0.40 ml/min flow rate onto a GE Superdex 200 5/150 column at 25°C. 29 successive 1 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.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 242.6, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 0.01162, "pddf_i0_error": 1.64e-05, "guinier_i0": 0.011686, "guinier_i0_error": null, "pddf_rg": 4.49, "pddf_rg_error": 0.05, "guinier_rg": 4.558, "guinier_rg_error": 0.256, "pddf_dmax": 12.6, "pddf_dmax_error": 0.1, "porod_volume": 363.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 2, "guinier_point_last": 47, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDVG6_datloglog_img.png", "symmetry": null, "last_modified": "2024-12-23T09:54:52.986675+01:00", "bragg_peak": [] }