{ "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": [] }