{"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":[]}