{ "code": "SASDCP2", "status": "Published", "type_of_curve": "Single concentration", "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/SASDCP2.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCP2.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCP2_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCP2_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCP2_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCP2_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCP2.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=6", "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "Tandem CBD from Clostridium histolyticum ColG collagenase at pCa 6", "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": "2015-09-14", "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": null, "concentration_max": 5.0, "sample_volume": null, "flow_rate": null, "s_min": 0.084, "s_max": 5.579, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCP2_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/SASDCP2_fit1_model1.pdb", "model_mw": 24.57, "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/SASDCP2_fit1_fit_img.png", "software": "DAMMIF", "chi_square_value": 1.59, "p_value": 0.0, "fit_residual_plot": "SASDCP2_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCP2_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 6 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 = 4πsinθ/λ and 2θ is the scattering angle). One solute concentration of 5.00 mg/ml was measured at 10°C. The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering of the solvent-blank was subtracted.", "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": 265.1, "pddf_i0_error": 0.6, "guinier_i0": 261.8, "guinier_i0_error": 0.4, "pddf_rg": 2.71, "pddf_rg_error": 0.02, "guinier_rg": 2.56, "guinier_rg_error": 0.1, "pddf_dmax": 12.8, "pddf_dmax_error": null, "porod_volume": 32.8, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 31, "guinier_point_last": 65, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDCP2_datloglog_img.png", "symmetry": null, "last_modified": "2020-07-03T15:10:24.071469+02:00", "bragg_peak": [] }