{
"code": "SASDUV3",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/nm",
"project": {
"title": "The crystal structure of the N-terminal domain of the backbone pilin LrpA reveals a new closure-and-twist motion for assembling dynamic pili in Ligilactobacillus ruminis",
"publication": {
"title": "The crystal structure of the N-terminal domain of the backbone pilin LrpA reveals a new closure-and-twist motion for assembling dynamic pili in Ligilactobacillus ruminis",
"author_list": "Prajapati A, Palva A, von Ossowski I, Krishnan V",
"journal": "Acta Crystallographica Section D Structural Biology",
"doi": "10.1107/S2059798324005114",
"pmid": null,
"published_date": "2024 Jun 27"
},
"status": "released",
"submitted_date": "2024-03-06",
"released_date": "2024-07-03"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDUV3.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDUV3.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUV3_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUV3_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDUV3_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUV3_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDUV3.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 6M",
"resolution": null
},
"name": "PETRA III",
"city": "DESY; Hamburg",
"country": "Germany",
"beamline_name": "EMBL P12",
"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": "LPXTG-motif cell wall anchor domain protein",
"short_name": "LrpA",
"sequence": "MGRDPNSETSTETATVTLHKYVFDKSLPSDKIDNSKSQDEINAWLTKNNAE\r\nALDGVEFTAYDVTSEYADAYKTATGDKNESPADAAKTASAAVAKKADALQKT\r\nATVVGKQTTANGGLASFANLPLRDANGNYKAYLFAETDAPANITQKAEPFV\r\nLAMPIYGADGKTVQKSINIYPKNVKQSDKKTLNDNRSHHDFTAGEKINYSIE\r\nTVVPWNIANKKVYTITDNPSKGLIMDADTIQIEGLASNKYTVKKNADNGFTIT\r\nIPAANLAAFAGKTLKTTVKGHLSIEDLTLIDTGIPNKATAKVDNEAHHEVKSEE\r\nVFTGGKKFVKVDGSNQSKTLAGAQFQLVIVKNGQVVKYAHGNEKDGYTFD\r\nTNNTNVATKTTGENGQFEFAGLKYSESLEAGESYAVKEVKAPTGYDLLKDPV\r\nLFTVTKDSYKTVQAADGQKISNTKKGGFLPLEHHHHHH",
"organism": "Ligilactobacillus ruminis ATCC 25644",
"uniprot_code": "E7FRT5",
"uniprot_range_first": 35,
"uniprot_range_last": 472,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MKNHKKLRNALATLLLALPLALQGAVGVKTAQAAETSTETATVTLHKYVFDKSLPSDKID\nNSKSQDEINAWLTKNNAEALDGVEFTAYDVTSEYADAYKTATGDKNESPADAAKTASAAV\nAKKADALQKTATVVGKQTTANGGLASFANLPLRDANGNYKAYLFAETDAPANITQKAEPF\nVLAMPIYGADGKTVQKSINIYPKNVKQSDKKTLNDNRSHHDFTAGEKINYSIETVVPWNI\nANKKVYTITDNPSKGLIMDADTIQIEGLASNKYTVKKNADNGFTITIPAANLAAFAGKTL\nKTTVKGHLSIEDLTLIDTGIPNKATAKVDNEAHHEVKSEEVFTGGKKFVKVDGSNQSKTL\nAGAQFQLVIVKNGQVVKYAHGNEKDGYTFDTNNTNVATKTTGENGQFEFAGLKYSESLEA\nGESYAVKEVKAPTGYDLLKDPVLFTVTKDSYKTVQAADGQKISNTKKGGFLPSTGGMGIV\nLFIAAGVVVMAGAAGTMIVRRNRRENI",
"mw": 48.969,
"total_mw": 48.969,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "LrpA backbone-Pilin Subunit from Ligilactobacillus ruminis. The protein construct used for SAXS contains a C-terminal polyhistidine tag (LEHHHHHH) and an additional non-native amino acid sequence at the N-terminus (MGRDPNS)."
}
],
"buffer": {
"name": "20 mM Tris-HCl, 150 mM NaCl",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 8.0,
"deuteration": null
},
"purity_method": null,
"name": "SAXS analysis of the LrpA backbone-Pilin Subunit from Ligilactobacillus ruminis",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "RCB",
"address": "Haryana, India",
"full_name": "Regional Centre for Biotechnology",
"webpage": "http://www.rcb.res.in/"
}
],
"contributor_name": "Vengadesan",
"contributor_surname": "Krishnan",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2021-11-01",
"storage_temperature": 20.0,
"cell_temperature": 20.0,
"exposure_time": 0.5,
"number_of_frames": 15,
"wavelength": 0.123983,
"sample_detector_distance": 3.0,
"concentration_min": null,
"concentration_max": 5.0,
"sample_volume": 40.0,
"flow_rate": 3.0,
"s_min": 0.185,
"s_max": 3.348,
"total_exposure_time": null,
"seccolumn": 49
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDUV3_fit1_model1_img.png",
"software": "AlphaFold",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDUV3_fit1_model1.pdb",
"model_mw": 47.0,
"bead_radius": null,
"log": null,
"symmetry": "P1",
"comment": null,
"user": 245
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDUV3_fit1_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.435,
"p_value": 0.0,
"fit_residual_plot": "SASDUV3_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDUV3_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/lrpa_sec_ph8_lrpa_alpha.log",
"software_version": "ATSAS 3.2.1",
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDUV3_fit2_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "ATSAS 3.2.1",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDUV3_fit2_model1.cif",
"model_mw": null,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/lrpa-ph8_7.log",
"symmetry": "P1",
"comment": null,
"user": 245
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDUV3_fit2_fixed_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 1.117,
"p_value": 0.0447,
"fit_residual_plot": "SASDUV3_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDUV3_fit2.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/lrpa-ph8_7.log",
"software_version": "ATSAS 3.2.1",
"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 the LrpA backbone-Pilin Subunit in 20 mM Tris-HCl, 150 mM NaCl, pH 8 were collected on the EMBL P12 beam line at PETRA III (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.123983 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 40.00 μl sample at 5 mg/ml was injected at a 3.00 ml/min flow rate onto a Cytiva Superdex 200 Increase 5/150 column at 20°C. 15 successive 0.500 second frames were collected through the SEC sample elution peak. 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": 49.0,
"experimental_mw_error": null,
"guinier_i0_mw": 49.0,
"guinier_i0_mw_error": null,
"porod_mw": 37.5,
"porod_mw_error": null,
"pddf_i0": 349.5,
"pddf_i0_error": null,
"guinier_i0": 354.139,
"guinier_i0_error": null,
"pddf_rg": 3.494,
"pddf_rg_error": null,
"guinier_rg": 3.47,
"guinier_rg_error": 0.03,
"pddf_dmax": 10.59,
"pddf_dmax_error": null,
"porod_volume": 59.13,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 7,
"guinier_point_last": 69,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDUV3_datloglog_img.png",
"symmetry": null,
"last_modified": "2024-07-03T09:35:08.121331+02:00",
"bragg_peak": []
}