{ "code": "SASDDR3", "status": "Published", "type_of_curve": "Extrapolated to infinite dilution", "angular_unit": "1/A", "project": { "title": "Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition.", "publication": { "title": "Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition.", "author_list": "Hirata A, Okada K, Yoshii K, Shiraishi H, Saijo S, Yonezawa K, Shimizu N, Hori H", "journal": "Nucleic Acids Res", "doi": "10.1093/nar/gkz856", "pmid": "31586407", "published_date": "2019 Oct 5" }, "status": "released", "submitted_date": "2018-02-27", "released_date": "2019-10-06" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDR3.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDR3.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDR3_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDR3_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDR3_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDR3_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDR3.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus3 2M", "resolution": 0.172 }, "name": "Photon Factory (PF), High Energy Accelerator Research Organization (KEK)", "city": "Tsukuba", "country": "Japan", "beamline_name": "BL-10C", "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": "Trm7: tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase", "short_name": "Trm7_yeast", "sequence": "MGKSSKDKRDLYYRKAKEQGYRARSAFKLLQLNDQFHFLDDPNLKRVVDLCAAPGSWSQVLSRKLFDESPSSDKEDRKIVSVDLQPMSPIPHVTTLQADITHPKTLARILKLFGNEKADFVCSDGAPDVTGLHDLDEYVQQQLIMSALQLTACILKKGGTFVAKIFRGRDIDMLYSQLGYLFDKIVCAKPRSSRGTSLEAFIVCLGYNPPSNWTPKLDVNTSVDEFFQGCFLNKLCISDKLSHWNEEERNIAEFMACGSLQSFDSDATYHDLPSSVAGTSSSLDPVQSPTNPPYKKALELKRSGKLTRSVLEVLFQGPSHHHHHH", "organism": "Saccharomyces cerevisiae", "uniprot_code": "P38238", "uniprot_range_first": 1, "uniprot_range_last": 310, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MGKSSKDKRDLYYRKAKEQGYRARSAFKLLQLNDQFHFLDDPNLKRVVDLCAAPGSWSQV\nLSRKLFDESPSSDKEDRKIVSVDLQPMSPIPHVTTLQADITHPKTLARILKLFGNEKADF\nVCSDGAPDVTGLHDLDEYVQQQLIMSALQLTACILKKGGTFVAKIFRGRDIDMLYSQLGY\nLFDKIVCAKPRSSRGTSLEAFIVCLGYNPPSNWTPKLDVNTSVDEFFQGCFLNKLCISDK\nLSHWNEEERNIAEFMACGSLQSFDSDATYHDLPSSVAGTSSSLDPVQSPTNPPYKKALEL\nKRSGKLTRSV", "mw": 36.494, "total_mw": 36.494, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "Trm734: Regulator of Ty1 transposition protein 10", "short_name": "Trm734 (WDR6_yeast)", "sequence": "MKDLSHYGPALCVKFYNDYVLAGYGPFIHVYDYHSATLINKCRLFHYNKVHGLSLSSEGKILAYGARSVTIVELEDVLKKESLVDFERINSDWITGATFSFDNLQIYLLTCYNKVLICDLNCEVLFRKSLGGERSILYSGIIKVFGPDKVYVNAGTVMGGVIIWDLFSETKIHNLLGHEGSIFYVNLSNNGRYVASCSDDRSIRLWDLETGKQLSVGWSHTARIWNLMFFDNDSKLISVSEDCTCRVWNIIESRENVAELSISNVYEVHLIKSIWGVDVKDDEMIAVTSGNDGRLKLIDLLQLKRHGDEETSFSLDDIAKQCGDIFEKNESIKGFQWFSFGVIAITSLGKILKYSDVTKQWKLLLTNEKFNSYPITNGIQTQNIAVFSNNKSDILLIKFSKDSADIIETEEFHLDELSKTNNCLVTEYDDDSFLLTLQSPNPREKFVCLEISLQNLKIKSKHCFNKPENFSSSCLTSFRNHILVGSRFSTLVIYNLLDESEEPFIIRRLSPGDTTTSIEFVEDKDNSAVFSVTNRDGYYVFIELTKNSLEEGPYRLSYKVLHSNKMMKGFLEGAFFNSKGEYITYGFKSSLFYLYNETNCYELASEVCGGSHRLWNLAKITDGHVLMYIKASRFHLRKIYNSIVPETLENGVHGREIRDISICPVSNTNTNDNFKDGHIFCTASEDTTIKLGYFNNRTGKVQNFWTQRKHVSGLQRCQFINHKLMISSSAREELFLWELNDKYNKRPYMTIRQALPVSTNNSDLRIMDFDVKFISQSGDFLLVTVYSDSTIKIWHYRENQNKFDLIMQGRYKTCCLFNVVFIALKEELLVVISPTDGHLVVYNITEYVPFSVDPISGDLVDHKLDATISNLPAPVAQLPVHQSGVKSLDYVANATRTSATILTGGDDNGLGLSNLKLDDSNKVTLKTSDFIAAAASSTITSGMLINGGKEVITTSVDQVIRAWEITAGKLSLVDKKRTTVADTGSLEIISNDEDADSEKTLLIGGVGLSIWKKLEVLFQGPSHHHHHH", "organism": "Saccharomyces cerevisiae", "uniprot_code": "Q08924", "uniprot_range_first": 1, "uniprot_range_last": 1013, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MKDLSHYGPALCVKFYNDYVLAGYGPFIHVYDYHSATLINKCRLFHYNKVHGLSLSSEGK\nILAYGARSVTIVELEDVLKKESLVDFERINSDWITGATFSFDNLQIYLLTCYNKVLICDL\nNCEVLFRKSLGGERSILYSGIIKVFGPDKVYVNAGTVMGGVIIWDLFSETKIHNLLGHEG\nSIFYVNLSNNGRYVASCSDDRSIRLWDLETGKQLSVGWSHTARIWNLMFFDNDSKLISVS\nEDCTCRVWNIIESRENVAELSISNVYEVHLIKSIWGVDVKDDEMIAVTSGNDGRLKLIDL\nLQLKRHGDEETSFSLDDIAKQCGDIFEKNESIKGFQWFSFGVIAITSLGKILKYSDVTKQ\nWKLLLTNEKFNSYPITNGIQTQNIAVFSNNKSDILLIKFSKDSADIIETEEFHLDELSKT\nNNCLVTEYDDDSFLLTLQSPNPREKFVCLEISLQNLKIKSKHCFNKPENFSSSCLTSFRN\nHILVGSRFSTLVIYNLLDESEEPFIIRRLSPGDTTTSIEFVEDKDNSAVFSVTNRDGYYV\nFIELTKNSLEEGPYRLSYKVLHSNKMMKGFLEGAFFNSKGEYITYGFKSSLFYLYNETNC\nYELASEVCGGSHRLWNLAKITDGHVLMYIKASRFHLRKIYNSIVPETLENGVHGREIRDI\nSICPVSNTNTNDNFKDGHIFCTASEDTTIKLGYFNNRTGKVQNFWTQRKHVSGLQRCQFI\nNHKLMISSSAREELFLWELNDKYNKRPYMTIRQALPVSTNNSDLRIMDFDVKFISQSGDF\nLLVTVYSDSTIKIWHYRENQNKFDLIMQGRYKTCCLFNVVFIALKEELLVVISPTDGHLV\nVYNITEYVPFSVDPISGDLVDHKLDATISNLPAPVAQLPVHQSGVKSLDYVANATRTSAT\nILTGGDDNGLGLSNLKLDDSNKVTLKTSDFIAAAASSTITSGMLINGGKEVITTSVDQVI\nRAWEITAGKLSLVDKKRTTVADTGSLEIISNDEDADSEKTLLIGGVGLSIWKK", "mw": 116.254, "total_mw": 116.254, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50 mM HEPES, 200 mM KCl, 5% v/v Glycerol, 10mM β-mercaptoethanol", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "Yeast tRNA Nm34 methyltransferase Trm7-Trm734 complex from Sacharomyces cerevisiae", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "KEK", "address": "Tsukuba, Japan", "full_name": "High Energy Accelerater Research Organization (KEK)", "webpage": "https://www.kek.jp" } ], "contributor_name": "Kento", "contributor_surname": "Yonezawa", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2015-12-16", "storage_temperature": 20.0, "cell_temperature": 20.0, "exposure_time": 20.0, "number_of_frames": 40, "wavelength": 0.1, "sample_detector_distance": 2.05, "concentration_min": 0.47, "concentration_max": 3.1, "sample_volume": null, "flow_rate": null, "s_min": 0.063, "s_max": 4.099, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDR3_fit1_model1_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDDR3_fit1_model1.pdb", "model_mw": 141.44, "bead_radius": 4.25, "log": "https://www.sasbdb.org/media/log_files/zc_001_xuZHpHZ.log", "symmetry": "P1", "comment": null, "user": 275 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDR3_fit1_fixed_fit_img.png", "software": "DAMMIF", "chi_square_value": 1.917, "p_value": 0.034809, "fit_residual_plot": "SASDDR3_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDR3_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/zc_001_cMEHJMB.log", "software_version": "ATSAS 2.7", "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDR3_fit2_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/SASDDR3_fit2_model1.pdb", "model_mw": 145.3, "bead_radius": 1.9, "log": "https://www.sasbdb.org/media/log_files/TRM04.log", "symmetry": "P1", "comment": null, "user": 275 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDR3_fit2_fixed_fit_img.png", "software": "CORAL", "chi_square_value": 2.18, "p_value": 8e-06, "fit_residual_plot": "SASDDR3_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDR3_fit2.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/TRM04.log", "software_version": "ATSAS 2.7", "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of Yeast tRNA Nm34 methyltransferase Trm7-Trm734 complex in 50 mM HEPES-KOH, 200 mM, KCl, 5 % v/v glycerol, 10 mM β-mercaptoethanol, pH 8.0 were collected on the beam line BL-10C at the Phton Factory (PF; Tsukuba, Ibaraki, Japan) using a Pilatus3 2M detector at a sample-detector distance of 2.05 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). 40 images of 20 second frames were collected at 20°C. The data were normalized to the intensity of the incident beam and circularly averaged; the scattering of the solvent-blank was subtracted. The extrapolated scattering profile at a concentration of zero was calculated PRIMUS QT of ATSAS.", "tags": [], "intensity_unit": "1/cm", "experimental_mw": 158.819, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 136.25, "porod_mw_error": null, "pddf_i0": 0.1921, "pddf_i0_error": 0.0001, "guinier_i0": 0.192981, "guinier_i0_error": 0.0001, "pddf_rg": 3.77, "pddf_rg_error": 0.003, "guinier_rg": 3.79, "guinier_rg_error": 0.003, "pddf_dmax": 12.99, "pddf_dmax_error": null, "porod_volume": 218.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 7, "guinier_point_last": 54, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDDR3_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }