{"code":"SASDWG9","status":"Published","type_of_curve":"Single concentration","angular_unit":"1/A","project":{"title":"A class III ligand oscillates between internal and terminal binding modes as it engages with the Dishevelled PDZ domain.","publication":{"title":"A class III ligand oscillates between internal and terminal binding modes as it engages with the Dishevelled PDZ domain.","author_list":"Kumar J, Micka M, Komárek J, Klumpler T, Bystrý V, Sprangers R, Bařinka C, Bryja V, Tripsianes K","journal":"Structure","doi":"10.1016/j.str.2025.05.012","pmid":"40516532","published_date":"2025 Jun 5"},"status":"released","submitted_date":"2025-02-25","released_date":"2025-06-17"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDWG9.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDWG9.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWG9_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWG9_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDWG9_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWG9_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDWG9.sascif","experiment":{"instrument":{"detector":{"type":"Hybrid Photon Counting (HPC) X-ray detector","name":"Rigaku HyPix-3000","resolution":100.0},"name":"CEITEC","city":"Brno","country":"Czech Republic","beamline_name":"Rigaku BioSAXS-2000","beam_geometry":null,"type_of_source":"X-ray in house","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":"Segment polarity protein dishevelled homolog DVL-3","short_name":"DLV3_PDZ","sequence":"GAMALNIITVTLNMEKYNFLGISIVGQSNERGDGGIYIGSIMKGGAVAADGRIEPGDMLLQVNEINFENMSNDDAVRVLREIVHKPGPITLTVAKCWDPSPRGCFTLPRSE","organism":"Homo sapiens","uniprot_code":"Q92997","uniprot_range_first":245,"uniprot_range_last":351,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MGETKIIYHLDGQETPYLVKLPLPAERVTLADFKGVLQRPSYKFFFKSMDDDFGVVKEEI\nSDDNAKLPCFNGRVVSWLVSAEGSHPDPAPFCADNPSELPPPMERTGGIGDSRPPSFHPH\nAGGGSQENLDNDTETDSLVSAQRERPRRRDGPEHATRLNGTAKGERRREPGGYDSSSTLM\nSSELETTSFFDSDEDDSTSRFSSSTEQSSASRLMRRHKRRRRKQKVSRIERSSSFSSITD\nSTMSLNIITVTLNMEKYNFLGISIVGQSNERGDGGIYIGSIMKGGAVAADGRIEPGDMLL\nQVNEINFENMSNDDAVRVLREIVHKPGPITLTVAKCWDPSPRGCFTLPRSEPIRPIDPAA\nWVSHTAAMTGTFPAYGMSPSLSTITSTSSSITSSIPDTERLDDFHLSIHSDMAAIVKAMA\nSPESGLEVRDRMWLKITIPNAFIGSDVVDWLYHNVEGFTDRREARKYASNLLKAGFIRHT\nVNKITFSEQCYYIFGDLCGNMANLSLHDHDGSSGASDQDTLAPLPHPGAAPWPMAFPYQY\nPPPPHPYNPHPGFPELGYSYGGGSASSQHSEGSRSSGSNRSGSDRRKEKDPKAGDSKSGG\nSGSESDHTTRSSLRGPRERAPSERSGPAASEHSHRSHHSLASSLRSHHTHPSYGPPGVPP\nLYGPPMLMMPPPPAAMGPPGAPPGRDLASVPPELTASRQSFRMAMGNPSEFFVDVM","mw":11.978,"total_mw":11.978,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":"PDZ domain of the Segment polarity protein dishevelled homolog DVL-3. The protein construct used for SAXS contains an additional four non-native amino acids at the N-terminus (GAMA)."}],"buffer":{"name":"50 mM sodium phosphate, 50 mM NaCl, 0.5 mM EDTA","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":6.5,"deuteration":null},"purity_method":null,"name":"PDZ domain of the segment polarity protein dishevelled homolog DVL-3","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":null,"address":null,"full_name":"CEITEC - Central European Institute of Technology, Masaryk University","webpage":"https://www.ceitec.eu/"}],"contributor_name":"Tomas","contributor_surname":"Klumpler","orcid":null}],"concentration_method":null,"concentration_unit":null,"date":"2021-01-27","storage_temperature":4.0,"cell_temperature":25.0,"exposure_time":600.0,"number_of_frames":6,"wavelength":0.154,"sample_detector_distance":0.48,"concentration_min":null,"concentration_max":5.0,"sample_volume":null,"flow_rate":null,"s_min":0.123,"s_max":4.002,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDWG9_fit1_model1_img.png","software":"REFMAC","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":"5.8.0258","model_data":"https://www.sasbdb.org/media/pdb_file/SASDWG9_fit1_model1.pdb","model_mw":11.77,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":195}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWG9_fit1_fixed_fit_img.png","software":"CRYSOL","chi_square_value":0.989,"p_value":0.0321,"fit_residual_plot":"SASDWG9_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDWG9_fit1.fit","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/DVL3_PDZext_C8_chainA00.log","software_version":"ATSAS 2.8.3","description":""}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"5.0","i0_calibration_standard":null,"description":null,"experiment_description":"SAXS data from solutions of PDZ domain of the segment polarity protein dishevelled homolog DVL-3 in 50 mM sodium phosphate, 50 mM NaCl, 0.5 mM EDTA, pH 6.5 were collected using a Rigaku BioSAXS-2000 instrument at CEITEC (Brno, Czech Republic) equipped with a Rigaku HyPix-3000 detector at a sample-detector distance of 0.5 m and at a wavelength of λ = 0.154 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 25°C. Six successive 600 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.","tags":[],"intensity_unit":"arbitrary","experimental_mw":10.4,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":12.6,"porod_mw_error":null,"pddf_i0":0.7841,"pddf_i0_error":null,"guinier_i0":0.79546,"guinier_i0_error":null,"pddf_rg":1.57,"pddf_rg_error":null,"guinier_rg":1.609,"guinier_rg_error":0.14,"pddf_dmax":4.31,"pddf_dmax_error":null,"porod_volume":20.2,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":1,"guinier_point_last":48,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDWG9_datloglog_img.png","symmetry":null,"last_modified":"2025-06-17T09:21:01.066938+02:00","bragg_peak":[]}