{ "code": "SASDDW4", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/nm", "project": { "title": "Molecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3.", "publication": { "title": "Molecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3.", "author_list": "Scietti L, Chiapparino A, De Giorgi F, Fumagalli M, Khoriauli L, Nergadze S, Basu S, Olieric V, Cucca L, Banushi B, Profumo A, Giulotto E, Gissen P, Forneris F", "journal": "Nat Commun", "doi": "10.1038/s41467-018-05631-5", "pmid": "30089812", "published_date": "2018 Aug 8" }, "status": "released", "submitted_date": "2018-03-09", "released_date": "2018-08-13" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDW4.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDW4.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDW4_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDW4_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDW4_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDW4_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDW4.sascif", "experiment": { "instrument": { "detector": { "type": "Dectris", "name": "Pilatus 1M", "resolution": 172.0 }, "name": "ESRF", "city": "Grenoble", "country": "France", "beamline_name": "BM29", "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": "Procollagen lysyl hydroxylase LH3", "short_name": "LH3", "sequence": "SSDRPRGRDPVNPEKLLVITVATAETEGYLRFLRSAEFFNYTVRTLGLGEEWRGGDVARTV\r\nGGGQKVRWLKKEMEKYADREDMIIMFVDSYDVILAGSPTELLKKFVQSGSRLLFSAESFC\r\nWPEWGLAEQYPEVGTGKRFLNSGGFIGFATTIHQIVRQWKYKDDDDDQLFYTRLYLDPGL\r\nREKLSLNLDHKSRIFQNLNGALDEVVLKFDRNRVRIRNVAYDTLPIVVHGNGPTKLQLNY\r\nLGNYVPNGWTPEGGCGFCNQDRRTLPGGQPPPRVFLAVFVEQPTPFLPRFLQRLLLLDYP\r\nPDRVTLFLHNNEVFHEPHIADSWPQLQDHFSAVKLVGPEEALSPGEARDMAMDLCRQDPE\r\nCEFYFSLDADAVLTNLQTLRILIEENRKVIAPMLSRHGKLWSNFWGALSPDEYYARSEDY\r\nVELVQRKRVGVWNVPYISQAYVIRGDTLRMELPQRDVFSGSDTDPDMAFCKSFRDKGIFL\r\nHLSNQHEFGRLLATSRYDTEHLHPDLWQIFDNPVDWKEQYIHENYSRALEGEGIVEQPCP\r\nDVYWFPLLSEQMCDELVAEMEHYGQWSGGRHEDSRLAGGYENVPTVDIHMKQVGYEDQWL\r\nQLLRTYVGPMTESLFPGYHTKARAVMNFVVRYRPDEQPSLRPHHDSSTFTLNVALNHKGL\r\nDYEGGGCRFLRYDCVISSPRKGWALLHPGRLTHYHEGLPTTWGTRYIMVSFVDPAAA", "organism": "Homo sapiens", "uniprot_code": "O60568", "uniprot_range_first": 25, "uniprot_range_last": 738, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MTSSGPGPRFLLLLPLLLPPAASASDRPRGRDPVNPEKLLVITVATAETEGYLRFLRSAE\nFFNYTVRTLGLGEEWRGGDVARTVGGGQKVRWLKKEMEKYADREDMIIMFVDSYDVILAG\nSPTELLKKFVQSGSRLLFSAESFCWPEWGLAEQYPEVGTGKRFLNSGGFIGFATTIHQIV\nRQWKYKDDDDDQLFYTRLYLDPGLREKLSLNLDHKSRIFQNLNGALDEVVLKFDRNRVRI\nRNVAYDTLPIVVHGNGPTKLQLNYLGNYVPNGWTPEGGCGFCNQDRRTLPGGQPPPRVFL\nAVFVEQPTPFLPRFLQRLLLLDYPPDRVTLFLHNNEVFHEPHIADSWPQLQDHFSAVKLV\nGPEEALSPGEARDMAMDLCRQDPECEFYFSLDADAVLTNLQTLRILIEENRKVIAPMLSR\nHGKLWSNFWGALSPDEYYARSEDYVELVQRKRVGVWNVPYISQAYVIRGDTLRMELPQRD\nVFSGSDTDPDMAFCKSFRDKGIFLHLSNQHEFGRLLATSRYDTEHLHPDLWQIFDNPVDW\nKEQYIHENYSRALEGEGIVEQPCPDVYWFPLLSEQMCDELVAEMEHYGQWSGGRHEDSRL\nAGGYENVPTVDIHMKQVGYEDQWLQLLRTYVGPMTESLFPGYHTKARAVMNFVVRYRPDE\nQPSLRPHHDSSTFTLNVALNHKGLDYEGGGCRFLRYDCVISSPRKGWALLHPGRLTHYHE\nGLPTTWGTRYIMVSFVDP", "mw": 90.0, "total_mw": 180.0, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "25 mM HEPES, 200 mM NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "Procollagen lysyl hydroxylase LH3 measured using SEC-SAXS", "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": "2018-02-28", "storage_temperature": 20.0, "cell_temperature": 20.0, "exposure_time": 1.0, "number_of_frames": 75, "wavelength": 0.09919, "sample_detector_distance": 2.87, "concentration_min": null, "concentration_max": 3.5, "sample_volume": null, "flow_rate": null, "s_min": 0.051, "s_max": 4.928, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDW4_fit3_model1_img.png", "software": "GASBOR", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDDW4_fit3_model1.pdb", "model_mw": null, "bead_radius": 1.9, "log": null, "symmetry": null, "comment": null, "user": 294 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDW4_fit3_fit_img.png", "software": "GASBOR", "chi_square_value": 1.85, "p_value": 0.0, "fit_residual_plot": "SASDDW4_fit3_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDW4_fit3.fir", "fit_log": null, "software_version": null, "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": "The sample was injected at a load concentration of 3.5 mg/mL. The SEC column used was a Superdex 200 PC 3.2/300 Increase (GE Healthcare) at a flow rate 0.075 mL/min.", "experiment_description": "Synchrotron SAXS data from solutions of procollagen lysyl hydroxylase LH3 in 25 mM HEPES, 200 mM NaCl, pH 8 were measured at 20°C using SEC-SAXS collected on the BM29 beam line at the ESRF storage ring (Grenoble, France) equipped with a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.09919 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.50 mg/ml was injected onto the column. 75 successive 1 second frames were collected through the sample elution peak and processed using CHROMIXS that included the identification and subtraction of an appropriate solvent-blank.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 180.0, "experimental_mw_error": null, "guinier_i0_mw": 184.0, "guinier_i0_mw_error": 6.0, "porod_mw": 170.0, "porod_mw_error": null, "pddf_i0": 62.4, "pddf_i0_error": 0.1, "guinier_i0": 61.5, "guinier_i0_error": 0.12, "pddf_rg": 5.346, "pddf_rg_error": 0.02, "guinier_rg": 5.05, "guinier_rg_error": 0.07, "pddf_dmax": 20.96, "pddf_dmax_error": null, "porod_volume": 268.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 9, "guinier_point_last": 43, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDDW4_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }