The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
Every source field is expanded here, including empty values, list members and fields already shown above.
View the complete summary.json source
{
"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": []
}
