{"code":"SASDEX6","status":"Published","type_of_curve":"Single concentration","angular_unit":"1/A","project":{"title":"Structural interpretations of a flexible cold-active AMS8 lipase by combining small-angle X-ray scattering and molecular dynamics simulation (SAXS-MD).","publication":{"title":"Structural interpretations of a flexible cold-active AMS8 lipase by combining small-angle X-ray scattering and molecular dynamics simulation (SAXS-MD).","author_list":"Yaacob N, Kamonsutthipaijit N, Soontaranon S, Leow TC, Rahman RNZRA, Ali MSM","journal":"Int J Biol Macromol","doi":"10.1016/j.ijbiomac.2022.08.145","pmid":"36029961","published_date":"2022 Aug 24"},"status":"released","submitted_date":"2018-10-27","released_date":"2021-09-20"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDEX6.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDEX6.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEX6_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEX6_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEX6_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEX6_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDEX6.sascif","experiment":{"instrument":{"detector":{"type":null,"name":"MAR 345 Image Plate","resolution":null},"name":"Synchrotron Light Research Institute (SLRI)","city":"Nakhon Ratchasima","country":"Thailand","beamline_name":"BL1.3W","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":"LipAMS8","short_name":"AMS8","sequence":">tr|E1B2U7|E1B2U7_9PSED LipAMS8 OS=Pseudomonas sp. AMS8 OX=882519 PE=4 SV=1\r\nMGVFDYKNLGTEGSKALFADAMAITLYSYHNLDNGFAVGYQHNGFGLGLPATLVGALLGS\r\nTDSQGVIPGIPWNPDSEKAALEAVNKAGWTPISASTLGYGGKVDARGTFFGEKAGYTTAQ\r\nVEVLGKYDGDGKLLEIGIGFRGTSGPRETLITDSIGDLVSDLLAALGPKDYAKNYAGEAF\r\nGTLLKDVAAYAGSHGLTGKDVVVSGHSLGGLAVNSMADLSGNKWSGFYKDSNYVAYASPT\r\nQSSGDKVLNIGYENDPVFRALDGSSFNFSSLGVHDKPHESTTDNIVSFNDHYASTLWNVL\r\nPFSIVNVPTWLSHLPTGYGDGLTRVLDSKFYDLTSRDSTIIVANLSDPARANTWVQDLNR\r\nNAEPHKGNTFIIGSDGNDLIQGGKGVDFIEGGKGNDTIRDNSGHNTFLFGGQFGQDRVIG\r\nYQSTDKLVFKDVEGSADWRDHAKVVGGDTVLSFGADSVTLVGVGLAGVGGDGISIS","organism":"Pseudomonas sp. AMS8","uniprot_code":"E1B2U7","uniprot_range_first":1,"uniprot_range_last":476,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MGVFDYKNLGTEGSKALFADAMAITLYSYHNLDNGFAVGYQHNGFGLGLPATLVGALLGS\nTDSQGVIPGIPWNPDSEKAALEAVNKAGWTPISASTLGYGGKVDARGTFFGEKAGYTTAQ\nVEVLGKYDGDGKLLEIGIGFRGTSGPRETLITDSIGDLVSDLLAALGPKDYAKNYAGEAF\nGTLLKDVAAYAGSHGLTGKDVVVSGHSLGGLAVNSMADLSGNKWSGFYKDSNYVAYASPT\nQSSGDKVLNIGYENDPVFRALDGSSFNFSSLGVHDKPHESTTDNIVSFNDHYASTLWNVL\nPFSIVNVPTWLSHLPTGYGDGLTRVLDSKFYDLTSRDSTIIVANLSDPARANTWVQDLNR\nNAEPHKGNTFIIGSDGNDLIQGGKGVDFIEGGKGNDTIRDNSGHNTFLFGGQFGQDRVIG\nYQSTDKLVFKDVEGSADWRDHAKVVGGDTVLSFGADSVTLVGVGLAGVGGDGISIS","mw":50.019,"total_mw":50.019,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"50 mM Tris HCl, 5 mM CaCl2","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":8.0,"deuteration":null},"purity_method":null,"name":"Cold-active AMS8 lipase in the presence of calcium (without polyhistidine affinity tag)","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":null,"address":"Thailand","full_name":"Synchrotron Light Research Institute","webpage":"https://www.slri.or.th"}],"contributor_name":"Norhayati","contributor_surname":"Yaacob","orcid":null}],"concentration_method":null,"concentration_unit":null,"date":"2018-03-06","storage_temperature":10.0,"cell_temperature":25.0,"exposure_time":600.0,"number_of_frames":1,"wavelength":0.138,"sample_detector_distance":1.7,"concentration_min":null,"concentration_max":2.0,"sample_volume":null,"flow_rate":null,"s_min":0.214,"s_max":3.742,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDEX6_fit1_model1_img.png","software":"DAMMIF","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":"r10552","model_data":"https://www.sasbdb.org/media/pdb_file/SASDEX6_fit1_model1.pdb","model_mw":53.421,"bead_radius":2.5,"log":null,"symmetry":"P1","comment":null,"user":314}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEX6_fit1_fixed_fit_img.png","software":"DAMMIF","chi_square_value":1.921,"p_value":0.033735,"fit_residual_plot":"SASDEX6_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDEX6_fit1.fir","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/S_AMS8-1.log","software_version":"r10552","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 cold-active AMS8 lipase (without polyhistidine affinity tag) in 50 mM Tris HCl, 5 mM CaCl2, pH 8 were collected on the BL1.3W SAXS/WAXS beam line at the Synchrotron Light Research Institute (SLRI; Nakhon Ratchasima, Thailand) using a MAR 345 Image Plate detector at a sample-detector distance of 1.7 m and at a wavelength of λ = 0.138 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 2.00 mg/ml was measured at 25°C. One 600 second frame was 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":50.0,"experimental_mw_error":null,"guinier_i0_mw":40.1,"guinier_i0_mw_error":0.0,"porod_mw":54.0,"porod_mw_error":null,"pddf_i0":81.58,"pddf_i0_error":null,"guinier_i0":77.71,"guinier_i0_error":0.52,"pddf_rg":3.04,"pddf_rg_error":null,"guinier_rg":2.859,"guinier_rg_error":0.021,"pddf_dmax":9.8,"pddf_dmax_error":null,"porod_volume":86.8,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":37,"guinier_point_last":115,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDEX6_datloglog_img.png","symmetry":null,"last_modified":"2022-08-30T18:12:26.610492+02:00","bragg_peak":[]}