{"code":"SASDVW3","status":"Published","type_of_curve":"SEC-SAS","angular_unit":"1/A","project":{"title":"Structural basis for recruitment of peptidoglycan endopeptidase MepS by lipoprotein NlpI.","publication":{"title":"Structural basis for recruitment of peptidoglycan endopeptidase MepS by lipoprotein NlpI.","author_list":"Wang S, Huang CH, Lin TS, Yeh YQ, Fan YS, Wang SW, Tseng HC, Huang SJ, Chang YY, Jeng US, Chang CI, Tzeng SR","journal":"Nat Commun","doi":"10.1038/s41467-024-49552-y","pmid":"38937433","published_date":"2024 Jun 27"},"status":"released","submitted_date":"2024-06-29","released_date":"2024-07-04"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDVW3.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDVW3.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVW3_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVW3_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVW3_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVW3_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDVW3.sascif","experiment":{"instrument":{"detector":{"type":null,"name":"Eiger X 1M & 9M","resolution":0.001},"name":"NSRRC","city":"Hsinchu","country":"Taiwan","beamline_name":"TPS13A","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":"Lipoprotein NlpI","short_name":"NlpI","sequence":"MSNTSWRKSEVLAVPLQPTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSDKEQWGWNIVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANNVHNFVEHRYALLELSLLGQDQDDLAESDQQ","organism":"Escherichia coli (strain K12)","uniprot_code":"P0AFB1","uniprot_range_first":20,"uniprot_range_last":294,"oligomerization":"dimer","molecular_type":"protein","uniprot_sequence":"MKPFLRWCFVATALTLAGCSNTSWRKSEVLAVPLQPTLQQEVILARMEQILASRALTDDE\nRAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFD\nSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDPNDPFRSLWLYLAEQKLDEK\nQAKEVLKQHFEKSDKEQWGWNIVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYL\nGKYYLSLGDLDSATALFKLAVANNVHNFVEHRYALLELSLLGQDQDDLAESDQQ","mw":31.641,"total_mw":63.282,"number_molecules":2,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":"Lipoprotein NlpI."},{"long_name":"Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase","short_name":"MepS","sequence":"MSANNTAKNMHPETRAVGSETSSLQASQDEFENLVRNVDVKSRIMDQYADWKGVRYRLGGSTKKGIDCSGFVQRTFREQFGLELPRSTYEQQEMGKSVSRSNLRTGDLVLFRAGSTGRHVGIYIGNNQFVHASTSSGVIISSMNEPYWKKRYNEARRVLSRS","organism":"Escherichia coli (strain K12)","uniprot_code":"P0AFV4","uniprot_range_first":28,"uniprot_range_last":188,"oligomerization":"tetramer","molecular_type":"protein","uniprot_sequence":"MVKSQPILRYILRGIPAIAVAVLLSACSANNTAKNMHPETRAVGSETSSLQASQDEFENL\nVRNVDVKSRIMDQYADWKGVRYRLGGSTKKGIDCSGFVQRTFREQFGLELPRSTYEQQEM\nGKSVSRSNLRTGDLVLFRAGSTGRHVGIYIGNNQFVHASTSSGVIISSMNEPYWKKRYNE\nARRVLSRS","mw":18.292,"total_mw":73.168,"number_molecules":4,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":""}],"buffer":{"name":"0.2 M Na/K phosphate pH 7.0, 2 mM 2-mercaptoethanol","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":7.0,"deuteration":null},"purity_method":null,"name":"Lipoprotein NlpI dimer bound to two asymmetrical murein DD-endopeptidase mMepS dimers at pH 7.0","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":null,"address":null,"full_name":"Institute of biochemistry and molecular biology,  College of Medicine, National Taiwan University.","webpage":null}],"contributor_name":"Shen","contributor_surname":"Wang","orcid":"https://orcid.org/0000-0002-3700-8853"}],"concentration_method":null,"concentration_unit":null,"date":"2023-09-07","storage_temperature":10.0,"cell_temperature":10.0,"exposure_time":2.0,"number_of_frames":210,"wavelength":0.0826,"sample_detector_distance":2.499,"concentration_min":null,"concentration_max":10.0,"sample_volume":100.0,"flow_rate":0.2,"s_min":0.066,"s_max":6.173,"total_exposure_time":null,"seccolumn":10},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDVW3_fit1_model1_img.png","software":"PyMOL","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDVW3_fit1_model1.pdb","model_mw":125.4,"bead_radius":null,"log":"https://www.sasbdb.org/media/log_files/NM_1_2.log","symmetry":null,"comment":null,"user":1020}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVW3_fit1_fixed_fit_img.png","software":"CRYSOL","chi_square_value":1.725,"p_value":0.0,"fit_residual_plot":"SASDVW3_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDVW3_fit1.fit","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/NM_1_2_yGWzZdj.log","software_version":null,"description":""}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"5.0","i0_calibration_standard":null,"description":"Note: There is a discrepancy between the calculated molecular weight of the fully formed complex (136 kDa) compared to the experimentally determined molecular weight (117 kDa).","experiment_description":"Synchrotron SAXS data from solutions of NlpI dimer bound to two asymmetrical mMepS dimers in 0.2 M Na/K phosphate pH 7.0, 2 mM 2-mercaptoethanol, were collected on the TPS13A beam line at the NSRRC (Hsinchu, Taiwan) using a Eiger X 1M & 9M detector at a sample-detector distance of 2.5 m and at a wavelength of λ = 0.0826 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 100.00 μl sample at 10 mg/ml was injected at a 0.20 ml/min flow rate onto a Agilent Bio SEC-3, 300 Å column at 10°C. 210 successive 2 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":"1/cm","experimental_mw":117.0,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":76.0,"porod_mw_error":null,"pddf_i0":0.03213,"pddf_i0_error":0.0002365,"guinier_i0":0.0327544,"guinier_i0_error":null,"pddf_rg":3.5,"pddf_rg_error":0.32,"guinier_rg":3.51,"guinier_rg_error":0.568,"pddf_dmax":11.5,"pddf_dmax_error":null,"porod_volume":123.13,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":9,"guinier_point_last":131,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDVW3_datloglog_img.png","symmetry":null,"last_modified":"2024-07-04T12:04:37.091963+02:00","bragg_peak":[]}