{ "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": [] }