{ "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": [] }