{ "code": "SASDEZ9", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/nm", "project": { "title": "Structure of a collagen VI α3 chain VWA domain array: adaptability and functional implications of myopathy causing mutations", "publication": { "title": "Structure of a collagen VI α3 chain VWA domain array: adaptability and functional implications of myopathy causing mutations", "author_list": "Solomon-Degefa H, Gebauer J, Jeffries C, Freiburg C, Meckelburg P, Bird L, Baumann U, Svergun D, Owens R, Werner J, Behrmann E, Paulsson M, Wagener R", "journal": "Journal of Biological Chemistry", "doi": "10.1074/jbc.RA120.014865", "pmid": null, "published_date": "2020 Jul 21" }, "status": "released", "submitted_date": null, "released_date": "2020-07-25" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEZ9.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEZ9.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEZ9_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEZ9_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEZ9_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEZ9_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEZ9.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 6M", "resolution": null }, "name": "PETRA III", "city": "DESY; Hamburg", "country": "Germany", "beamline_name": "EMBL P12", "beam_geometry": null, "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": "Collagen, type VI, alpha 3", "short_name": "N6N3", "sequence": "MAHHHHHHSSGSWSHPQFEKGGGSGGGSGGGSWSHPQFEKSSGLEVLFQGP\r\nESKRDILFLFDGSVNVLGQFPAVRDFLYRIIEELDVKPDGTRVAIAQFSD\r\nDVRLESRFSEHQTKAEILNLVKKMKLKTGKALNLGYALDYALRNIFVRSA\r\nGSRIEDNVQQFLVLLVAGRSSDAVAGPASSLKQRGVVPFIFQAKNANPSE\r\nLEQIVLSPAFILAAESLPKIGDLQSQIVSLLKAEQGSGPVSGEKDVVFLI\r\nDGSEGVRSGFPLLKDFVQRVVESLDVGPDRVRVALVQYSDRTRPEFYLNS\r\nHMDQQGVISAIRRLTLLGGPTPNTGAALEFVLRNILTSSTGSRIAEGVPQ\r\nLLIVLTAEPSGDDVRGPSVVLKQGGAVPIGIGIGNADISEMQTISFIPDF\r\nAVAIPTFRELGTIQQVISERVIQLNREELSSLKPILTPSTGAGVGSKKDV\r\nVFLIDGSRNAGPEFQYIRTLIERIVEYLDIGFDTTRVAVIQFSEDSKMEF\r\nPLNAHFSKDEVQNAVRRLRPKGGSQVYIGNALEYVLKNIFQRPLGSRIEE\r\nGVPQFLVLISSGKSDDEVDDSAVELKQFGVAPLTIARHTDQEELVKISLS\r\nPEYVYSVSTFRELPRLEQKLLTPITTLTSQQIHQILASTRYPPSVVESDA\r\nADIVFLIDSSDAVKPDGIAHIRDFVSRIVRRLNIGPSKVRIGVVQFSNDV\r\nFPEFYLKTHKSQSSVLEAIRRLRFKGGSPLNTGRALEFVARNLFVKSAGS\r\nRIEDGVPQHLVLFLGGKSQDDVARHAQVISSSGIVSLGIGDRNIDRTDLQ\r\nTITNDPRLVFTVREFRELPNIEERVMLSFGPSGATPQPPGVDLPSPSRP", "organism": "Mus musculus", "uniprot_code": "D3YWD1", "uniprot_range_first": 831, "uniprot_range_last": 1630, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MRKHRHLPLVAVFSLLLSGIATTHAQQHGDVKNGAAADIVFLVDSSWSAGKDRFLLVQEF\nLSDVVESLAVGDNDFHFALVRLNGNPHTEFLLNTYHSKQEVLSHIVNMSYIGGSNQTGKG\nLEYVIHSHLTEASGSRAADGVPQVIIVLTDGQSEDGFALPSAELKSADVNVFAVGVEGAD\nERALGEVASEPLSMHVFNLENVTSLHGLVGNLVSCIHSSVNPERAGDKESLKDITAQDSA\nDIIFLIDGSQNTGNANFDVIRDFLVNVLERLSVGNQQVQVGVVQYSEEPITMFSLNSYPS\nKAAVLDAVKGLSLVGGESANIGQALDFVVENHFTRAGGSRVEEGVPQVLVLISAGPSSDE\nIRDSVVALKQASVFSFGLGAQAASRAELQHIATDDSLVFTVPEFRSFGDLQEQILPYLVG\nVAQRHIVLQPPAIVTQVMEVNKRDIVFLVDGSSSLGPSNFNAIRDFVTRVIQRLEIGQDL\nVQVSVAQYADTVKPEFYLNSYTNKRDAITAVRKMRALNGSALYTGSSLDFVRNNLFTSSA\nGHRAAEGVPKLLVLITGGKSLDEVSQPAQELKRGSIMALAVGSKAADEDELKEIAFDSSL\nVFIPAEFRPAPLQNMLPSLMAPLRTLTGTTEVHVNKRDIIFLLDGSDNVGKNNFPYVRDF\nVTNLVNSLDVGSDNIRVGLVQFSDTPVTEFSLDTYQTKSELLAHLRRLQLKGGSGLNAGS\nALSYIHANHFTEAGGSRTREHVPQLLLLLMAGPSEDAYLQAANALVRSGVLTFCVGTNRA\nDKAELEHIAFNPSLVYLMDDFRSLPSLPQQLIQPLTTYVSGGVQEVPLSQPESKRDILFL\nFDGSVNVLGQFPAVRDFLYRIIEELDVKPDGTRVAIAQFSDDVRLESRFSEHQTKAEILN\nLVKKMKLKTGKALNLGYALDYALRNIFVRSAGSRIEDNVQQFLVLLVAGRSSDAVAGPAS\nSLKQRGVVPFIFQAKNANPSELEQIVLSPAFILAAESLPKIGDLQSQIVSLLKAEQGSGP\nVSGEKDVVFLIDGSEGVRSGFPLLKDFVQRVVESLDVGPDRVRVALVQYSDRTRPEFYLN\nSHMDQQGVISAIRRLTLLGGPTPNTGAALEFVLRNILTSSTGSRIAEGVPQLLIVLTAEP\nSGDDVRGPSVVLKQGGAVPIGIGIGNADISEMQTISFIPDFAVAIPTFRELGTIQQVISE\nRVIQLNREELSSLKPILTPSTGAGVGSKKDVVFLIDGSRNAGPEFQYIRTLIERIVEYLD\nIGFDTTRVAVIQFSEDSKMEFPLNAHFSKDEVQNAVRRLRPKGGSQVYIGNALEYVLKNI\nFQRPLGSRIEEGVPQFLVLISSGKSDDEVDDSAVELKQFGVAPLTIARHTDQEELVKISL\nSPEYVYSVSTFRELPRLEQKLLTPITTLTSQQIHQILASTRYPPSVVESDAADIVFLIDS\nSDAVKPDGIAHIRDFVSRIVRRLNIGPSKVRIGVVQFSNDVFPEFYLKTHKSQSSVLEAI\nRRLRFKGGSPLNTGRALEFVARNLFVKSAGSRIEDGVPQHLVLFLGGKSQDDVARHAQVI\nSSSGIVSLGIGDRNIDRTDLQTITNDPRLVFTVREFRELPNIEERVMLSFGPSGATPQPP\nGVDLPSPSRPEKKKADIVFLLDGSINFRRDSFQEVLRFASEIVDTVYEDGDSIRVGLVQY\nNSDPTDEFFLRDFSTKRQIIDAI", "mw": 92.936, "total_mw": 92.936, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM TRIS, 150mM NaCl 3% v/v glycerol", "concentration_unit": null, "comment": "The TRIS buffer is pH first, then add additional components are added without further pH adjustment", "additive": null, "concentration": null, "pka": null, "ph": 7.4, "deuteration": null }, "purity_method": null, "name": "Collagen VI von Willebrand factor (VWA) four-domain fragment, N6N3", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "EMBL-Hamburg", "address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany", "full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation", "webpage": "http://www.embl-hamburg.de/index.php" } ], "contributor_name": "Cy M", "contributor_surname": "Jeffries", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2018-11-04", "storage_temperature": 20.0, "cell_temperature": 20.0, "exposure_time": 1.0, "number_of_frames": 50, "wavelength": 0.124, "sample_detector_distance": 3.0, "concentration_min": null, "concentration_max": 7.0, "sample_volume": null, "flow_rate": null, "s_min": 0.061, "s_max": 7.003, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEZ9_fit1_model1_img.png", "software": "CORAL", "pdb_link": [ { "pdb_code": "4igi", "ext_code": "4IGI", "ext_type": "pdb", "difference_with_model": "derived" } ], "model_title": null, "type_of_model": "mix", "software_version": "5", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEZ9_fit1_model1.pdb", "model_mw": 93.59, "bead_radius": 1.9, "log": "https://www.sasbdb.org/media/log_files/07N6N3.log", "symmetry": "P1", "comment": null, "user": 9 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEZ9_fit1_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 1.02, "p_value": 0.553966, "fit_residual_plot": "SASDEZ9_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEZ9_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/07N6N300.log", "software_version": "2.8.3", "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEZ9_fit2_model1_img.png", "software": "BUNCH", "pdb_link": [], "model_title": null, "type_of_model": "mix", "software_version": "8", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEZ9_fit2_model1.pdb", "model_mw": 93.57, "bead_radius": 1.9, "log": "https://www.sasbdb.org/media/log_files/N6N3Q.log", "symmetry": "P1", "comment": null, "user": 9 } ], "fit_unit": "1/A", "fit_plot": 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"p_value": 0.863635, "fit_residual_plot": "SASDEZ9_fit3_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEZ9_fit3.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/N6B.log", "software_version": "2.3i", "description": "" }, { "models": [], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEZ9_fit4_fixed_fit_img.png", "software": "EOM/GAJOE", "chi_square_value": 0.975, "p_value": 0.8998, "fit_residual_plot": "SASDEZ9_fit4_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEZ9_fit4.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/logFile_001_1_cw2kJv9.log", "software_version": null, "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "4.6", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of Collagen VI von Willebrand factor (VWA) four-domain fragment, N6N3 in 20 mM TRIS, 150mM NaCl 3% v/v glycerol, pH 7.4 were collected on the EMBL P12 camera at the PETRA III storage ring (Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). SEC-SAXS was performed at 20°C using the following parameters: Column: GE-Healthcare S200 Increase 10/300 analytical SEC column; Flow rate: 0.6 mL/min; Sample injection concentration: 7 mg/mL; Injection volume: 75 μL. Total X-ray acquisition time = 2400 s. The data were collected through the SEC peak of the protein as a series of 50 x 1 second exposures and processed using CHROMIXS (Panjkovich & Svergun, 2018 Bioinformatics 34(11):1944-1946) that was also used to select an appropriate matched solvent-blank. Parallel inline multi-angle laser and dynamic light scattering with refractive index measurements (SEC-MALLS/DLS/RI) were performed using a Wyatt Mini-Dawn TREOS with an in-built quasi elastic light scattering (QELS) module coupled to an OptiLab T-Rex refractometer. The quoted experiential MW for this entry is derived from MALLS. Concentration-independent MW estimates obtained directly from the SAXS data using DATMW (Hajizadeh et al., 2018 Scientific Reports 8, 7204), as part of CHROMIXS/ATSAS 2.8.3, as well as the SEC-MALLS/DLS/RI data and additional modelling files, including ITASSER homology modelling (Yang et al., 2015 Nature Methods 12, 7-8) are included in the full-entry zip archive.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 89.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 89.0, "porod_mw_error": null, "pddf_i0": 517.8, "pddf_i0_error": null, "guinier_i0": 514.54, "guinier_i0_error": 1.1, "pddf_rg": 4.24, "pddf_rg_error": null, "guinier_rg": 4.12, "guinier_rg_error": 0.01, "pddf_dmax": 15.6, "pddf_dmax_error": null, "porod_volume": 143.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 93, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDEZ9_datloglog_img.png", "symmetry": null, "last_modified": "2023-06-21T07:55:24.740692+02:00", "bragg_peak": [] }