{"code":"SASDC54","status":"Published","type_of_curve":"Extrapolated to infinite dilution","angular_unit":"1/A","project":{"title":"Ca<sup>2+</sup> -induced orientation of tandem collagen binding domains from clostridial collagenase ColG permits two opposing functions of collagen fibril formation and retardation.","publication":{"title":"Ca<sup>2+</sup> -induced orientation of tandem collagen binding domains from clostridial collagenase ColG permits two opposing functions of collagen fibril formation and retardation.","author_list":"Caviness P, Bauer R, Tanaka K, Janowska K, Roeser JR, Harter D, Sanders J, Ruth C, Matsushita O, Sakon J","journal":"FEBS J","doi":"10.1111/febs.14611","pmid":"30035850","published_date":"2018 Sep"},"status":"released","submitted_date":"2017-05-26","released_date":"2018-03-28"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDC54.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDC54.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC54_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC54_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDC54_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC54_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDC54.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":"ColH protein","short_name":"ColH","sequence":"lpne\r\ngdsknslpyg kingtykgte kekikfsseg sfdpdgkivs yewdfgdgnk sneenpehsy\r\ndkvgtytvkl kvtddkgess vstttaeikd lsenklpviy mhvpksgaln qkvvfygkgt\r\nydpdgsiagy qwdfgdgsdf sseqnpshvy tkkgeytvtl rvmdssgqms ektmkikitd\r\npvypigteke pnnsketasg pivpgipvsg tientsdqdy fyfdvitpge vkidinklgy\r\nggatwvvyde nnnavsyatd dgqnlsgkfk adkpgryyih lymfngsymp yriniegsvg\r\nr","organism":"Hathewaya histolytica","uniprot_code":"Q46085","uniprot_range_first":717,"uniprot_range_last":1021,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MKRKCLSKRLMLAITMATIFTVNSTLPIYAAVDKNNATAAVQNESKRYTVSYLKTLNYYD\nLVDLLVKTEIENLPDLFQYSSDAKEFYGNKTRMSFIMDEIGRRAPQYTEIDHKGIPTLVE\nVVRAGFYLGFHNKELNEINKRSFKERVIPSILAIQKNPNFKLGTEVQDKIVSATGLLAGN\nETAPPEVVNNFTPILQDCIKNIDRYALDDLKSKALFNVLAAPTYDITEYLRATKEKPENT\nPWYGKIDGFINELKKLALYGKINDNNSWIIDNGIYHIAPLGKLHSNNKIGIETLTEVMKV\nYPYLSMQHLQSADQIKRHYDSKDAEGNKIPLDKFKKEGKEKYCPKTYTFDDGKVIIKAGA\nRVEEEKVKRLYWASKEVNSQFFRVYGIDKPLEEGNPDDILTMVIYNSPEEYKLNSVLYGY\nDTNNGGMYIEPEGTFFTYEREAQESTYTLEELFRHEYTHYLQGRYAVPGQWGRTKLYDND\nRLTWYEEGGAELFAGSTRTSGILPRKSIVSNIHNTTRNNRYKLSDTVHSKYGASFEFYNY\nACMFMDYMYNKDMGILNKLNDLAKNNDVDGYDNYIRDLSSNYALNDKYQDHMQERIDNYE\nNLTVPFVADDYLVRHAYKNPNEIYSEISEVAKLKDAKSEVKKSQYFSTFTLRGSYTGGAS\nKGKLEDQKAMNKFIDDSLKKLDTYSWSGYKTLTAYFTNYKVDSSNRVTYDVVFHGYLPNE\nGDSKNSLPYGKINGTYKGTEKEKIKFSSEGSFDPDGKIVSYEWDFGDGNKSNEENPEHSY\nDKVGTYTVKLKVTDDKGESSVSTTTAEIKDLSENKLPVIYMHVPKSGALNQKVVFYGKGT\nYDPDGSIAGYQWDFGDGSDFSSEQNPSHVYTKKGEYTVTLRVMDSSGQMSEKTMKIKITD\nPVYPIGTEKEPNNSKETASGPIVPGIPVSGTIENTSDQDYFYFDVITPGEVKIDINKLGY\nGGATWVVYDENNNAVSYATDDGQNLSGKFKADKPGRYYIHLYMFNGSYMPYRINIEGSVG\nR","mw":33.727,"total_mw":33.727,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null},{"long_name":"Collagenous Peptide model [(PPG)10]","short_name":null,"sequence":"PPGPPGPPGPPGPPGPPGPPGPPGPPGPPG","organism":"synthetic construct","uniprot_code":null,"uniprot_range_first":null,"uniprot_range_last":null,"oligomerization":"trimer","molecular_type":"protein","uniprot_sequence":null,"mw":3.21,"total_mw":9.63,"number_molecules":3,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"50 mM HEPES, 100 mM NaCl, 5 mM CaCl2","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":7.5,"deuteration":null},"purity_method":null,"name":"Envelope of Col H PKD-PKD-CBD complexed with mini-collagen","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":"Perry","contributor_surname":"Caviness","orcid":null}],"concentration_method":null,"concentration_unit":null,"date":"2016-10-12","storage_temperature":4.0,"cell_temperature":10.0,"exposure_time":0.3,"number_of_frames":33,"wavelength":0.113,"sample_detector_distance":null,"concentration_min":1.0,"concentration_max":5.0,"sample_volume":null,"flow_rate":null,"s_min":0.125,"s_max":3.575,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDC54_fit1_model1_img.png","software":"DAMMIF","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":"","model_data":"https://www.sasbdb.org/media/pdb_file/SASDC54_fit1_model1.pdb","model_mw":26.224,"bead_radius":2.5,"log":null,"symmetry":"","comment":"","user":217}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDC54_fit1_fit_img.png","software":"DAMMIF","chi_square_value":3.22,"p_value":3e-06,"fit_residual_plot":"SASDC54_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDC54_fit1.fir","fit_log":null,"software_version":"","description":null}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":null,"i0_calibration_standard":null,"description":"Scattering for samples with concentrations of 4 mg/ml, 3 mg/ml and 1 mg/ml were averaged. Each of the average scattering curves are used to extrapolate towards infinite dilution. The scattering curve at infinite dilution was used to generate the SAXS model that represents the averaged spatial disposition of the complex in solution (DAMFILT).","experiment_description":"Synchrotron SAXS data from solutions of the envelope of Col H PKD-PKD-CBD complexed with mini-collagen in 50 mM Hepes 100 mM NaCl 5 mM CaCl2, 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 wavelength of λ = 0.113 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Solute concentrations ranging between 1 and 5 mg/ml were measured at 10°C. 33 successive 0.300 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 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":46.613,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":null,"porod_mw_error":null,"pddf_i0":25.76,"pddf_i0_error":0.095,"guinier_i0":24.648,"guinier_i0_error":0.21,"pddf_rg":3.66,"pddf_rg_error":0.02,"guinier_rg":3.321,"guinier_rg_error":0.082,"pddf_dmax":14.16,"pddf_dmax_error":null,"porod_volume":38.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":4,"guinier_point_last":48,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDC54_datloglog_img.png","symmetry":null,"last_modified":"2020-08-20T10:59:17.177795+02:00","bragg_peak":[]}