{ "code": "SASDC72", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/A", "project": { "title": "High-resolution structure of the alcohol dehydrogenase domain of the bifunctional bacterial enzyme AdhE.", "publication": { "title": "High-resolution structure of the alcohol dehydrogenase domain of the bifunctional bacterial enzyme AdhE.", "author_list": "Azmi L, Bragginton EC, Cadby IT, Byron O, Roe AJ, Lovering AL, Gabrielsen M", "journal": "Acta Crystallogr F Struct Biol Commun", "doi": "10.1107/S2053230X20010237", "pmid": "32880589", "published_date": "2020 Sep 1" }, "status": "released", "submitted_date": "2017-05-11", "released_date": "2017-12-12" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDC72.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDC72.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC72_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC72_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDC72_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC72_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDC72.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": "Aldehyde-alcohol dehydrogenase", "short_name": "AdhE", "sequence": "MLWHKLPKSIYFRRGSLPIALDEVITDGHKRALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVIIALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTSG\r\nTGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMDMPKSLCAFGGLDAVTHAMEAYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFLGVCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIADHLGLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAFDDQCTGANPRYPLISELKQILLDTYYGRDYVEGETAAKKEAAPAKAEKKAKKSA", "organism": "Escherichia coli O157:H7", "uniprot_code": "P0A9Q8", "uniprot_range_first": 451, "uniprot_range_last": 891, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG\nIVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA\nIFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA\nLMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF\nDNGVICASEQSVVVVDSVYDAVRERFATHGGYLLQGKELKAVQDVILKNGALNAAIVGQP\nAYKIAELAGFSVPENTKILIGEVTVVDESEPFAHEKLSPTLAMYRAKDFEDAVEKAEKLV\nAMGGIGHTSCLYTDQDNQPARVSYFGQKMKTARILINTPASQGGIGDLYNFKLAPSLTLG\nCGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIALDEVITDGHK\nRALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVI\nIALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTSG\nTGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMDMPKSLCAFGGLDAVTHAME\nAYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFLG\nVCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIAD\nHLGLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAFDDQ\nCTGANPRYPLISELKQILLDTYYGRDYVEGETAAKKEAAPAKAEKKAKKSA", "mw": 48.33, "total_mw": 96.66, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM Tris 400 mM NaCl 5% v/v glycerol", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "Alcohol dehydrogenase from bifunctional alcohol/aldehyde dehydrogenase (P0A9Q8)", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Glasgow, Scotland, UK", "full_name": "University of Glasgow", "webpage": "http://www.gla.ac.uk/" } ], "contributor_name": "Liyana", "contributor_surname": "Azmi", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2015-11-27", "storage_temperature": 4.0, "cell_temperature": 4.0, "exposure_time": 1.0, "number_of_frames": 131, "wavelength": 0.1, "sample_detector_distance": 4.04, "concentration_min": null, "concentration_max": 10.0, "sample_volume": null, "flow_rate": null, "s_min": 0.045, "s_max": 4.017, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDC72_fit1_model1_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "r9217", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDC72_fit1_model1.pdb", "model_mw": 88.9, "bead_radius": 3.5, "log": "https://www.sasbdb.org/media/log_files/D2_AdhE.log", "symmetry": "P2", "comment": "", "user": 193 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDC72_fit1_model2_img.png", "software": "DAMFILT", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "5.0 r9217", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDC72_fit1_model2.pdb", "model_mw": 88.526, "bead_radius": 3.5, "log": null, "symmetry": "P2", "comment": "", "user": 193 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDC72_fit1_fixed_fit_img.png", "software": "DAMMIF", "chi_square_value": 1.85, "p_value": 0.2137, "fit_residual_plot": "SASDC72_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDC72_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/D2-AdhE1_9.log", "software_version": "r9217", "description": null } ], "estimated_volume_method": "DAMMIN", "pddf_software": "ATSAS GNOM", "pddf_software_version": "PRIMUS 2.7.1 GNOM", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data, I(s) vs s (s = 4π sin θ/λ, where 2θ is the scattering angle and λ is the X-ray wavelength) were collected from a sample of alcohol dehydrogenase from a bifunctional alcohol/aldehyde dehydrogenase protein (P0A9Q8) using continuous-flow size-exclusion chromatography SAXS (SEC-SAXS) on the B21 beam line at the Diamond Light Source (Oxfordshire, UK). Data (131 successive 1 second frames) were collected using a Pilatus 2M detector at a sample-detector distance of 4.0 m and at a wavelength of λ = 0.1 nm. The SEC mobile phase consisted of 20 mM Tris, 400 mM NaCl, 5% v/v glycerol, pH 7.5 (4°C) with a sample injection concentration of 10 mg/ml. Data obtained from solute-free eluates and SEC-elution peak were normalized to the intensity of the transmitted beam and radially averaged. The scattering of the solvent-blank was subtracted from the SEC-peak frames using ScÅtter and then analysed using Primus to produce the data displayed in this entry.", "tags": [], "intensity_unit": null, "experimental_mw": 91.4, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 0.0627, "pddf_i0_error": 0.0001, "guinier_i0": 0.061, "guinier_i0_error": 7e-05, "pddf_rg": 3.55, "pddf_rg_error": 0.23, "guinier_rg": 3.24, "guinier_rg_error": 0.06, "pddf_dmax": 16.87, "pddf_dmax_error": null, "porod_volume": 146.0, "porod_volume_error": null, "estimated_volume": 178.0, "estimated_volume_error": null, "guinier_point_first": 36, "guinier_point_last": 130, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDC72_datloglog_img.png", "symmetry": null, "last_modified": "2021-01-04T12:08:43.215101+01:00", "bragg_peak": [] }