{"code":"SASDVZ2","status":"Published","type_of_curve":"SEC-SAS","angular_unit":"1/nm","project":{"title":"Molecular structure and enzymatic mechanism of the human collagen hydroxylysine galactosyltransferase GLT25D1/COLGALT1","publication":{"title":"Molecular structure and enzymatic mechanism of the human collagen hydroxylysine galactosyltransferase GLT25D1/COLGALT1","author_list":"De Marco M, Rai S, Scietti L, Mattoteia D, Liberi S, Moroni E, Pinnola A, Vetrano A, Iacobucci C, Santambrogio C, Colombo G, Forneris F","journal":"Nature Communications","doi":"10.1038/s41467-025-59017-5","pmid":null,"published_date":"2025 Apr 16"},"status":"released","submitted_date":"2024-06-21","released_date":"2025-03-19"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDVZ2.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDVZ2.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVZ2_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVZ2_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVZ2_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVZ2_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDVZ2.sascif","experiment":{"instrument":{"detector":{"type":null,"name":"Pilatus3 2M","resolution":0.172},"name":"ESRF","city":"Grenoble","country":"France","beamline_name":"BM29","beam_geometry":"point","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":"Procollagen galactosyltransferase 1","short_name":"GLT25D1","sequence":"GSAPPGADAYFPEERWSPESPLQAPRVLIALLA\r\nRNAAHALPTTLGALERLRHPRERTALWVATDHNMDNTSTVLREWLVAVKSLYHSVEWRPA\r\nEEPRSYPDEEGPKHWSDSRYEHVMKLRQAALKSARDMWADYILFVDADNLILNPDTLSLL\r\nIAENKTVVAPMLDSRAAYSNFWCGMTSQGYYKRTPAYIPIRKRDRRGCFAVPMVHSTFLI\r\nDLRKAASRNLAFYPPHPDYTWSFDDIIVFAFSCKQAEVQMYVCNKEEYGFLPVPLRAHST\r\nLQDEAESFMHVQLEVMVKHPPAEPSRFISAPTKTPDKMGFDEVFMINLRRRQDRRERMLR\r\nALQAQEIECRLVEAVDGKAMNTSQVEALGIQMLPGYRDPYHGRPLTKGELGCFLSHYNIW\r\nKEVVDRGLQKSLVFEDDLRFEIFFKRRLMNLMRDVEREGLDWDLIYVGRKRMQVEHPEKA\r\nVPRVRNLVEADYSYWTLAYVISLQGARKLLAAEPLSKMLPVDEFLPVMFDKHPVSEYKAH\r\nFSLRNLHAFSVEPLLIYPTHYTGDDGYVSDTETSVVWNNEHVKTDWDRAKSQKMREQQAL\r\nSREAKNSDVLQSPLDSAAAAA","organism":"Homo sapiens","uniprot_code":"Q8NBJ5","uniprot_range_first":30,"uniprot_range_last":618,"oligomerization":"dimer","molecular_type":"protein","uniprot_sequence":"MAAAPRAGRRRGQPLLALLLLLLAPLPPGAPPGADAYFPEERWSPESPLQAPRVLIALLA\nRNAAHALPTTLGALERLRHPRERTALWVATDHNMDNTSTVLREWLVAVKSLYHSVEWRPA\nEEPRSYPDEEGPKHWSDSRYEHVMKLRQAALKSARDMWADYILFVDADNLILNPDTLSLL\nIAENKTVVAPMLDSRAAYSNFWCGMTSQGYYKRTPAYIPIRKRDRRGCFAVPMVHSTFLI\nDLRKAASRNLAFYPPHPDYTWSFDDIIVFAFSCKQAEVQMYVCNKEEYGFLPVPLRAHST\nLQDEAESFMHVQLEVMVKHPPAEPSRFISAPTKTPDKMGFDEVFMINLRRRQDRRERMLR\nALQAQEIECRLVEAVDGKAMNTSQVEALGIQMLPGYRDPYHGRPLTKGELGCFLSHYNIW\nKEVVDRGLQKSLVFEDDLRFEIFFKRRLMNLMRDVEREGLDWDLIYVGRKRMQVEHPEKA\nVPRVRNLVEADYSYWTLAYVISLQGARKLLAAEPLSKMLPVDEFLPVMFDKHPVSEYKAH\nFSLRNLHAFSVEPLLIYPTHYTGDDGYVSDTETSVVWNNEHVKTDWDRAKSQKMREQQAL\nSREAKNSDVLQSPLDSAARDEL","mw":68.493,"total_mw":136.986,"number_molecules":2,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":"GLT25D1/COLGALT1 was produced recombinantly as a N-terminal 8xHis-SUMO fusion in E. coli. After initial affinity chromatography, the sample was subject to tag removal using His-tagged SUMO protease followed by reverse affinity chromatography and dialysis. The sample was then subject to anion exchange chromatography for further polishing, followed by gel filtration into a Superdex 200 Increase 10/300 GL (Cytiva), equilibrated with 25 mM HEPES/NaOH, 100 mM NaCl, pH 8.0. The sample was concentrated to 4 mg/mL in a 30 kDa MWCO Vivaspin Turbo centrifugal filter (Sartorius) and used for SEC-SAXS analysis"}],"buffer":{"name":"25 mM HEPES, 0.1 M NaCl","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":8.0,"deuteration":null},"purity_method":null,"name":"Human Collagen Galactosyltransferase GLT25D1/COLGALT1","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":null,"address":"Italy","full_name":"University of Pavia","webpage":"http://wcm-3.unipv.it"}],"contributor_name":"Federico","contributor_surname":"Forneris","orcid":null}],"concentration_method":null,"concentration_unit":null,"date":"2022-06-05","storage_temperature":10.0,"cell_temperature":20.0,"exposure_time":1.0,"number_of_frames":1200,"wavelength":0.099187,"sample_detector_distance":2.867,"concentration_min":null,"concentration_max":4.0,"sample_volume":50.0,"flow_rate":0.06,"s_min":0.131,"s_max":3.145,"total_exposure_time":null,"seccolumn":14},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDVZ2_fit1_model1_img.png","software":"CORAL","pdb_link":[],"model_title":null,"type_of_model":"mix","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDVZ2_fit1_model1.pdb","model_mw":134.6,"bead_radius":1.9,"log":null,"symmetry":"P1","comment":"UNK residues have been renumbered according to protein residue numbering","user":294}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVZ2_fit1_fixed_fit_img.png","software":"CORAL","chi_square_value":1.889999,"p_value":0.0,"fit_residual_plot":"SASDVZ2_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDVZ2_fit1.fit","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/glt_agai.log","software_version":null,"description":"The crystal structure of human full-length GLT25D1/COLGALT1 was subject to loop modeling using CORAL, to introduce the missing N- and C-terminal loops on the dimeric ensemble."}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":null,"i0_calibration_standard":null,"description":null,"experiment_description":null,"tags":[],"intensity_unit":"arbitrary","experimental_mw":136.0,"experimental_mw_error":null,"guinier_i0_mw":131.0,"guinier_i0_mw_error":10.0,"porod_mw":114.0,"porod_mw_error":null,"pddf_i0":null,"pddf_i0_error":null,"guinier_i0":22.9078,"guinier_i0_error":null,"pddf_rg":null,"pddf_rg_error":null,"guinier_rg":4.33,"guinier_rg_error":0.021,"pddf_dmax":13.97,"pddf_dmax_error":null,"porod_volume":184.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":10,"guinier_point_last":33,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDVZ2_datloglog_img.png","symmetry":null,"last_modified":"2025-04-16T23:25:08.209553+02:00","bragg_peak":[]}