{ "code": "SASDCN2", "status": "Published", "type_of_curve": "Extrapolated to infinite dilution", "angular_unit": "1/A", "project": { "title": "Structural characterization of bacterial collagenases", "publication": { "title": "Structural characterization of bacterial collagenases", "author_list": "Bauer R", "journal": "University of Arkansas PhD thesis", "doi": null, "pmid": null, "published_date": "2017 Aug" }, "status": "released", "submitted_date": "2017-04-08", "released_date": "2019-01-07" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDCN2.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCN2.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCN2_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCN2_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCN2_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCN2_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCN2.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus3 X 2M", "resolution": 172.0 }, "name": "Advanced Light Source (ALS)", "city": "Berkeley, CA", "country": "USA", "beamline_name": "12.3.1 (SIBYLS)", "beam_geometry": "", "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": "Class1 collagenase", "short_name": "tandem CBD", "sequence": "GSPGIPGTTTPITKEMEPNDDIKEANGPIVEGVTVKGDLNGSDDADTFYFDVKEDGDVTIELPYSGSSNFTWLVYKEGDDQNHIASGIDKNNSKVGTFKSTKGRHYVFIYKHDSASNISYSLNIKGLGNEKLKEKENNDSSDKATVIPNFNTTMQGSLLGDDSRDYYSFEVKEEGEVNIELDKKDEFGVTWTLHPESNINDRITYGQVDGNKVSNKVKLRPGKYYLLVYKYSGSGNYELRVNK", "organism": "Hathewaya histolytica", "uniprot_code": "Q9X721", "uniprot_range_first": 883, "uniprot_range_last": 1118, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MKKNILKILMDSYSKESKIQTVRRVTSVSLLAVYLTMNTSSLVLAKPIENTNDTSIKNVE\nKLRNAPNEENSKKVEDSKNDKVEHVKNIEEAKVEQVAPEVKSKSTLRSASIANTNSEKYD\nFEYLNGLSYTELTNLIKNIKWNQINGLFNYSTGSQKFFGDKNRVQAIINALQESGRTYTA\nNDMKGIETFTEVLRAGFYLGYYNDGLSYLNDRNFQDKCIPAMIAIQKNPNFKLGTAVQDE\nVITSLGKLIGNASANAEVVNNCVPVLKQFRENLNQYAPDYVKGTAVNELIKGIEFDFSGA\nAYEKDVKTMPWYGKIDPFINELKALGLYGNITSATEWASDVGIYYLSKFGLYSTNRNDIV\nQSLEKAVDMYKYGKIAFVAMERITWDYDGIGSNGKKVDHDKFLDDAEKHYLPKTYTFDNG\nTFIIRAGDKVSEEKIKRLYWASREVKSQFHRVVGNDKALEVGNADDVLTMKIFNSPEEYK\nFNTNINGVSTDNGGLYIEPRGTFYTYERTPQQSIFSLEELFRHEYTHYLQARYLVDGLWG\nQGPFYEKNRLTWFDEGTAEFFAGSTRTSGVLPRKSILGYLAKDKVDHRYSLKKTLNSGYD\nDSDWMFYNYGFAVAHYLYEKDMPTFIKMNKAILNTDVKSYDEIIKKLSDDANKNTEYQNH\nIQELADKYQGAGIPLVSDDYLKDHGYKKASEVYSEISKAASLTNTSVTAEKSQYFNTFTL\nRGTYTGETSKGEFKDWDEMSKKLDGTLESLAKNSWSGYKTLTAYFTNYRVTSDNKVQYDV\nVFHGVLTDNADISNNKAPIAKVTGPSTGAVGRNIEFSGKDSKDEDGKIVSYDWDFGDGAT\nSRGKNSVHAYKKAGTYNVTLKVTDDKGATATESFTIEIKNEDTTTPITKEMEPNDDIKEA\nNGPIVEGVTVKGDLNGSDDADTFYFDVKEDGDVTIELPYSGSSNFTWLVYKEGDDQNHIA\nSGIDKNNSKVGTFKSTKGRHYVFIYKHDSASNISYSLNIKGLGNEKLKEKENNDSSDKAT\nVIPNFNTTMQGSLLGDDSRDYYSFEVKEEGEVNIELDKKDEFGVTWTLHPESNINDRITY\nGQVDGNKVSNKVKLRPGKYYLLVYKYSGSGNYELRVNK", "mw": 27.055, "total_mw": 27.055, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "10 mM HEPES 100 mM NaCL, 2% glycerol", "concentration_unit": null, "comment": "0.2 mM EGTA pCa=5", "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "Tandem CBD from Clostridium histolyticum ColG collagenase at pCa 5", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Fayetteville, AR, USA", "full_name": "University of Arkansas", "webpage": "https://www.uark.edu/" } ], "contributor_name": "Ryan", "contributor_surname": "Bauer", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2016-09-14", "storage_temperature": 4.0, "cell_temperature": 10.0, "exposure_time": null, "number_of_frames": null, "wavelength": 0.1127, "sample_detector_distance": 1.5, "concentration_min": 1.0, "concentration_max": 5.0, "sample_volume": null, "flow_rate": null, "s_min": 0.084, "s_max": 5.584, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCN2_fit1_model1_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "2.6.1", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDCN2_fit1_model1.pdb", "model_mw": 23.502, "bead_radius": 2.25, "log": null, "symmetry": "P1", "comment": "", "user": 207 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCN2_fit1_fit_img.png", "software": "DAMMIF", "chi_square_value": 0.65, "p_value": 0.224, "fit_residual_plot": "SASDCN2_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCN2_fit1.fir", "fit_log": null, "software_version": "2.6.1", "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "ATSAS GNOM 2.6.1", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of the tandem CBD from ColG collagenase at pCa 5 in 10 mM HEPES 100 mM NaCL, 2% glycerol, pH 7.5 were collected on the 12.3.1 (SIBYLS) beam line at the Advanced Light Source (ALS, Berkeley, CA, USA) using a Pilatus3 X 2M detector at a sample-detector distance of 1.5 m and at a wavelength of λ = 0.1127 nm (I(s) vs s, where s = 4πsin θ/λ and 2θ is the scattering angle). Solute concentrations ranging between 1 and 5 mg/ml were measured at 10°C. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the different curves were scaled for protein concentration. The low angle data collected at lower concentrations were extrapolated to infinite dilution and merged with the higher concentration data to yield the final composite scattering curve.", "tags": [], "intensity_unit": null, "experimental_mw": 27.1, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 342.0, "pddf_i0_error": 0.8, "guinier_i0": 336.3, "guinier_i0_error": 0.8, "pddf_rg": 2.66, "pddf_rg_error": 0.01, "guinier_rg": 2.53, "guinier_rg_error": 0.2, "pddf_dmax": 9.4, "pddf_dmax_error": null, "porod_volume": 36.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 50, "guinier_point_last": 86, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDCN2_datloglog_img.png", "symmetry": null, "last_modified": "2020-07-03T15:10:24.071469+02:00", "bragg_peak": [] }