{ "code": "SASDCK3", "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/SASDCK3.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCK3.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCK3_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCK3_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCK3_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCK3_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCK3.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": "MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG\r\nIVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA\r\nIFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA\r\nLMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF\r\nDNGVICASEQSVVVVDSVYDAVRERFATHGGYLLQGKELKAVQDVILKNGALNAAIVGQP\r\nAYKIAELAGFSVPENTKILIGEVTVVDESEPFAHEKLSPTLAMYRAKDFEDAVEKAEKLV\r\nAMGGIGHTSCLYTDQDNQPARVSYFGQKMKTARILINTPASQGGIGDLYNFKLAPSLTLG\r\nCGSWGGNSISENVGPKHLINKKTVAHHHHHH", "organism": "Escherichia coli O157:H7", "uniprot_code": "P0A9Q8", "uniprot_range_first": 1, "uniprot_range_last": 445, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG\nIVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA\nIFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA\nLMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF\nDNGVICASEQSVVVVDSVYDAVRERFATHGGYLLQGKELKAVQDVILKNGALNAAIVGQP\nAYKIAELAGFSVPENTKILIGEVTVVDESEPFAHEKLSPTLAMYRAKDFEDAVEKAEKLV\nAMGGIGHTSCLYTDQDNQPARVSYFGQKMKTARILINTPASQGGIGDLYNFKLAPSLTLG\nCGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIALDEVITDGHK\nRALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVI\nIALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTSG\nTGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMDMPKSLCAFGGLDAVTHAME\nAYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFLG\nVCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIAD\nHLGLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAFDDQ\nCTGANPRYPLISELKQILLDTYYGRDYVEGETAAKKEAAPAKAEKKAKKSA", "mw": 48.038, "total_mw": 48.038, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "30 mM HEPES, 150 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": "Aldehyde dehydrogenase", "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": "2017-01-30", "storage_temperature": 4.0, "cell_temperature": 4.0, "exposure_time": 1.0, "number_of_frames": 18, "wavelength": 0.1, "sample_detector_distance": 4.04, "concentration_min": null, "concentration_max": 2.0, "sample_volume": null, "flow_rate": null, "s_min": 0.04, "s_max": 4.415, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCK3_fit1_model1_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDCK3_fit1_model1.pdb", "model_mw": 46.2, "bead_radius": 2.4, "log": "https://www.sasbdb.org/media/log_files/D1-AdhE1_7.log", "symmetry": "P1", "comment": "", "user": 193 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCK3_fit1_fixed_fit_img.png", "software": "DAMMIF", "chi_square_value": 1.774, "p_value": 0.4599, "fit_residual_plot": "SASDCK3_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCK3_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/D1-AdhE1_7.log", "software_version": "", "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCK3_fit2_model1_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/SASDCK3_fit2_model1.pdb", "model_mw": 46.036, "bead_radius": 2.5, "log": null, "symmetry": "P1", "comment": "this is the averaged representation of the model", "user": 193 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCK3_fit2_fixed_fit_img.png", "software": "DAMMIF", "chi_square_value": 1.773, "p_value": 0.4599, "fit_residual_plot": "SASDCK3_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCK3_fit2.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/D1-AdhE1_7_Es14JHH.log", "software_version": "", "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": null, "i0_calibration_standard": null, "description": "Aldehyde dehydrogenase (AldDH) is the N-terminal domain of the bifunctional alcohol/aldehyde dehydrogenase (AdhE; SASBDB entry SASDC72) spanning amino acids 1-445 of the full-length protein. SAXS data were measured from a protein construct that included a C-terminal 6 x histidine affinity chromatography tag. The buffer subtraction was performed using Scatter. Subsequent analysis was performed using PRIMUS (ATSAS 2.7.1).", "experiment_description": "Synchrotron SAXS data from solutions of aldehyde dehydrogenase in 30 mM HEPES, 150 mM NaCl, 5% (v/v) glycerol, pH 7.5 were collected on the B21 camera at the Diamond Light Source (Oxfordshire, UK) using a Pilatus 2M detector at a sample-detector distance of 4.0 m and at a wavelength of λ = 0.1 nm ((Is) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). One solute concentration of 2.00 mg/ml was measured at 4°C. 18 successive 1 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering of the solvent-blank was subtracted to obtain the SAXS profile displayed in this entry.", "tags": [], "intensity_unit": null, "experimental_mw": 46.5, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 46.5, "porod_mw_error": null, "pddf_i0": 0.1826, "pddf_i0_error": 0.0002068, "guinier_i0": 0.18, "guinier_i0_error": 0.00016, "pddf_rg": 2.74, "pddf_rg_error": 0.062, "guinier_rg": 2.68, "guinier_rg_error": 1.68, "pddf_dmax": 11.1, "pddf_dmax_error": null, "porod_volume": 74.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 20, "guinier_point_last": 182, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDCK3_datloglog_img.png", "symmetry": null, "last_modified": "2021-01-04T12:08:43.437315+01:00", "bragg_peak": [] }