{ "code": "SASDFB6", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/A", "project": { "title": "Protease-associated import systems are widespread in Gram-negative bacteria.", "publication": { "title": "Protease-associated import systems are widespread in Gram-negative bacteria.", "author_list": "Grinter R, Leung PM, Wijeyewickrema LC, Littler D, Beckham S, Pike RN, Walker D, Greening C, Lithgow T", "journal": "PLoS Genet", "doi": "10.1371/journal.pgen.1008435", "pmid": "31613892", "published_date": "2019 Oct" }, "status": "released", "submitted_date": "2019-05-08", "released_date": "2019-09-24" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFB6.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFB6.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFB6_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFB6_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFB6_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFB6_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFB6.sascif", "experiment": { "instrument": { "detector": { "type": "Dectris", "name": "Pilatus 1M", "resolution": 172.0 }, "name": "Australian Synchrotron", "city": "Melbourne", "country": "Australia", "beamline_name": "SAXS/WAXS", "beam_geometry": "Point", "type_of_source": "X-ray synchrotron", "point_source": true, "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": "Zinc protease PqqL", "short_name": null, "sequence": 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"uniprot_code": "P31828", "uniprot_range_first": 27, "uniprot_range_last": 931, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MEIIMRNLCFLLTLVATLLLPGRLIAAALPQDEKLITGQLDNGLRYMIYPHAHPKDQVNL\nWLQIHTGSLQEEDNELGVAHFVEHMMFNGTKTWPGNKVIETFESMGLRFGRDVNAYTSYD\nETVYQVSLPTTQKQNLQQVMAIFSEWSNAATFEKLEVDAERGVITEEWRAHQDAKWRTSQ\nARRPFLLANTRNLDREPIGLMDTVATVTPAQLRQFYQRWYQPNNMTFIVVGDIDSKEALA\nLIKDNLSKLPANKAAENRVWPTKAENHLRFNIINDKENRVNGIALYYRLPMVQVNDEQSF\nIEQAEWSMLVQLFNQRLQERIQSGELKTISGGTARSVKIAPDYQSLFFRVNARDDNMQDA\nANALMAELATIDQHGFSAEELDDVKSTRLTWLKNAVDQQAERDLRMLTSRLASSSLNNTP\nFLSPEETYQLSKRLWQQITVQSLAEKWQQLRKNQDAFWEQMVNNEVAAKKALSPAAILAL\nEKEYANKKLAAYVFPGRNLSLTVDADPQAEISSKETLAENLTSLTLSNGARVILAKSAGE\nEQKLQIIAVSNKGDLSFPAQQKSLIALANKAVSGSGVGELSSSSLKRWSAENSVTMSSKV\nSGMNTLLSVSARTNNPEPGFQLINQRITHSTINDNIWASLQNAQIQALKTLDQRPAEKFA\nQQMYETRYADDRTKLLQENQIAQFTAADALAADRQLFSSPADITFVIVGNVAEDKLVALI\nTRYLGSIKHSDSPLAAGKPLTRATDNASVTVKEQNEPVAQVSQWKRYDSRTPVNLPTRMA\nLDAFNVALAKDLRVNIREQASGAYSVSSRLSVDPQAKDISHLLAFTCQPERHDELLTLAN\nEVMVKRLAKGISEQELNEYQQNVQRSLDIQQRSVQQLANTIVNSLIQYDDPAAWTEQEQL\nLKQMTVENVNTAVKQYLSHPVNTYTGVLLPK", "mw": 101.744, "total_mw": 101.744, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM Tris HCl, 150 nM NaCl, 0.02 % NaN3, 5% glycerol", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.8, "deuteration": null }, "purity_method": null, "name": "The periplasmically localised protease PqqL from Escherichia coli", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Melbourne, Australia", "full_name": "Monash University", "webpage": "http://www.monash.edu/" } ], "contributor_name": "Grinter", "contributor_surname": "Grinter", "orcid": "https://orcid.org/0000-0002-8195-5348" } ], "concentration_method": null, "concentration_unit": null, "date": "2017-06-14", "storage_temperature": 20.0, "cell_temperature": 20.0, "exposure_time": 1.0, "number_of_frames": 10, "wavelength": 0.10322, "sample_detector_distance": 1.426, "concentration_min": null, "concentration_max": 8.0, "sample_volume": 100.0, "flow_rate": 0.4, "s_min": 0.057, "s_max": 3.188, "total_exposure_time": null, "seccolumn": 2 }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFB6_fit1_model1_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDFB6_fit1_model1.pdb", "model_mw": 116.37, "bead_radius": 3.5, "log": "https://www.sasbdb.org/media/log_files/PqqL_sub_sca_avg2-1.log", "symmetry": null, "comment": null, "user": 322 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFB6_fit1_model2_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "5", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDFB6_fit1_model2.pdb", "model_mw": 116.37, "bead_radius": 3.5, "log": "https://www.sasbdb.org/media/log_files/PqqL_sub_sca_avg2-1_cXdQQnM.log", "symmetry": "P1", "comment": null, "user": 322 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/PqqL_sub_sca_avg2-1_fixed_fit_img.png", "software": "DAMMIF", "chi_square_value": 0.506, "p_value": 0.003869, "fit_residual_plot": "PqqL_sub_sca_avg2-1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFB6_fit1.fir", "fit_log": null, "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFB6_fit2_model1_img.png", "software": "PDB (Protein Data Bank)", "pdb_link": [ { "pdb_code": "6ofs", "ext_code": "6OFS", "ext_type": "pdb", "difference_with_model": "identical" } ], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDFB6_fit2_model1.pdb", "model_mw": 101.9, "bead_radius": null, "log": "https://www.sasbdb.org/media/log_files/PqqL_FL_refine.log", "symmetry": "P1", "comment": null, "user": 322 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/PqqL_FL_refine_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 9.541, "p_value": 0.0, "fit_residual_plot": "PqqL_FL_refine_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFB6_fit2.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/PqqL_FL_refine.log", "software_version": null, "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 periplasmically localised protease (PqqL) from E. coli in 20 mM Tris HCl, 150 nM NaCl, 0.02 % NaN3, 5% glycerol, pH 7.8 were collected on the SAXS/WAXS beam line at the Australian Synchrotron (Melbourne, Australia) using a Pilatus 1M detector at a sample-detector distance of 1.4 m and at a wavelength of λ = 0.10322 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAXS was employed using a co-flow apparatus. The SEC parameters were as follows: A 100 μl sample at 8 mg/ml was injected onto a GE Superdex 200 Increase 5/150 column at 20°C. 10 successive 1 second frames were collected through the SEC 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": 113.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 130.0, "porod_mw_error": null, "pddf_i0": 0.08263, "pddf_i0_error": null, "guinier_i0": 0.13678, "guinier_i0_error": 0.0002, "pddf_rg": 4.11, "pddf_rg_error": null, "guinier_rg": 4.02, "guinier_rg_error": 0.88, "pddf_dmax": 13.69, "pddf_dmax_error": null, "porod_volume": 207.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 7, "guinier_point_last": 70, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDFB6_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }