{"code":"SASDX48","status":"Published","type_of_curve":"Single concentration","angular_unit":"1/A","project":{"title":"Crystal structure of a complete threonyl tRNA synthetase: toggle clamp model?","publication":{"title":"Crystal structure of a complete threonyl tRNA synthetase: toggle clamp model?","author_list":"Tran T, Fenwick M, Edwards T, Dranow D, Abendroth J, Shek R, Tillery L, Craig J, Van Voorhis W, Myler P","journal":"Biochemical and Biophysical Research Communications","doi":"10.1016/j.bbrc.2025.152677","pmid":null,"published_date":"2025 Sep"},"status":"released","submitted_date":"2025-08-22","released_date":"2025-09-22"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDX48.ift","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDX48.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX48_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX48_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDX48_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX48_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDX48.sascif","experiment":{"instrument":{"detector":{"type":null,"name":"Pilatus3 X 2M","resolution":172.0},"name":"Advanced Light Source (ALS)","city":"Berkeley, CA","country":"USA","beamline_name":"12.3.1 (SIBYLS)","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":"Stenotrophomonas maltophilia threonyl tRNA synthetase","short_name":"SmThrRS","sequence":">6VU9_1|Chain A|Threonine--tRNA ligase|Stenotrophomonas maltophilia (strain K279a) (522373)\r\nMAHHHHHHMINITLPDGSRREFENPVSVMEVAQSIGAGLAKATIAGAVDGVLVDASDVIDHDASLRIITAKDEEGVEIIRHSCAHLVGHAVKQLYPDVKMVIGPVIAEGFYYDIYSERPFTPDDMAAIEKRMGELIAQDYDVIKKMTPRAEVIEIFKARGEDYKLRLIEDMSEDIQAMGMYYHQEYVDMCRGPHVPNTRFLKAFKLTRISGAYWRGDAQNEQLQRIYGTAWADKKQLEAYIKRIEEAEMRDHRRIGKQQDLFHLQEEAPGLVFWHPKGWALWQVVEQYMRKVYRNSGYGEVRCPQILDVSLWKKSGHWDNYQDNMFFTESEKRTYAVKPMNCPGHIQVFNQGLHSYRDLPIRYGEFGSCHRNEPSGALHGILRVRGFTQDDGHVFCTENQIESEVTAFHQQALAVYQHFGFDEIQIKIALRPESRLGDDATWDKAEGALRSALTACGVEWQELPGEGAFYGPKIEYHLKDAIGRTWQLGTMQVDFMMPGRLGAEYVDENSQKKHPVMLHRAIVGSMERFLGILIEHHAGQFPAWLAPTQVVVANITDAQADYVSGVTKTLAEQGFRVSSDLRNEKIGYKIREHTLQRVPYLLVIGDREKENGAVAVRTRSGEDLGSMSLQAFIERLHAEGA","organism":null,"uniprot_code":"B2FN79","uniprot_range_first":null,"uniprot_range_last":null,"oligomerization":"dimer","molecular_type":"protein","uniprot_sequence":"MINITLPDGSRREFENPVSVMEVAQSIGAGLAKATIAGAVDGVLVDASDVIDHDASLRII\nTAKDEEGVEIIRHSCAHLVGHAVKQLYPDVKMVIGPVIAEGFYYDIYSERPFTPDDMAAI\nEKRMGELIAQDYDVIKKMTPRAEVIEIFKARGEDYKLRLIEDMSEDIQAMGMYYHQEYVD\nMCRGPHVPNTRFLKAFKLTRISGAYWRGDAQNEQLQRIYGTAWADKKQLEAYIKRIEEAE\nMRDHRRIGKQQDLFHLQEEAPGLVFWHPKGWALWQVVEQYMRKVYRNSGYGEVRCPQILD\nVSLWKKSGHWDNYQDNMFFTESEKRTYAVKPMNCPGHIQVFNQGLHSYRDLPIRYGEFGS\nCHRNEPSGALHGILRVRGFTQDDGHVFCTENQIESEVTAFHQQALAVYQHFGFDEIQIKI\nALRPESRLGDDATWDKAEGALRSALTACGVEWQELPGEGAFYGPKIEYHLKDAIGRTWQL\nGTMQVDFMMPGRLGAEYVDENSQKKHPVMLHRAIVGSMERFLGILIEHHAGQFPAWLAPT\nQVVVANITDAQADYVSGVTKTLAEQGFRVSSDLRNEKIGYKIREHTLQRVPYLLVIGDRE\nKENGAVAVRTRSGEDLGSMSLQAFIERLHAEGA","mw":72.937,"total_mw":145.874,"number_molecules":2,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":"Stenotrophomonas maltophilia threonyl tRNA synthetase with non-cleavable N-terminal purification tag 'MAHHHHHH'. The associated PDB entry is 6VU9. The first ten residues are modeled in all-atom format using Ranch, Pulchra, Scwrl, and Chimera. The Chimera morph tool was used to obtain an interpolation between the open and closed states in entries 6VU9 and 1QF6. The I vs q fit is an average of 100 fitted curves for 100 conformations based on this interpolation. The instance having the lowest chi squared value is also included."}],"buffer":{"name":"20 mM HEPES, 0.2 M NaCl, 1.5% v/v glycerol, and 1 mM TCEP","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":7.0,"deuteration":null},"purity_method":null,"name":"SmThrRS model based on PDB entries 6vu9 and 1qf6","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[],"concentration_method":null,"concentration_unit":null,"date":"2024-11-07","storage_temperature":4.0,"cell_temperature":20.0,"exposure_time":2.0,"number_of_frames":660,"wavelength":0.1127,"sample_detector_distance":2.1,"concentration_min":null,"concentration_max":3.1,"sample_volume":null,"flow_rate":null,"s_min":0.114,"s_max":4.707,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDX48_fit1_model1_img.png","software":"PDB (Protein Data Bank)","pdb_link":[{"pdb_code":"6vu9","ext_code":"6VU9","ext_type":"pdb","difference_with_model":"identical"}],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDX48_fit1_model1.pdb","model_mw":146.0,"bead_radius":null,"log":null,"symmetry":null,"comment":"Ensemble model","user":1185}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDX48_fit1_fixed_fit_img.png","software":"FoXS","chi_square_value":0.714975,"p_value":0.0,"fit_residual_plot":"SASDX48_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDX48_fit1.fit","fit_log":null,"software_version":null,"description":""},{"models":[],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDX48_fit2_fixed_fit_img.png","software":"FoXS","chi_square_value":0.60895,"p_value":0.0034,"fit_residual_plot":"SASDX48_fit2_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDX48_fit2.fit","fit_log":null,"software_version":null,"description":"Conformation having the lowest chi squared within the ensemble."}],"estimated_volume_method":null,"pddf_software":"BioXTAS RAW","pddf_software_version":null,"i0_calibration_standard":null,"description":"The trace was processed with Chromixs. The IFT was computed in BioXtas-RAW 2.3.0. The Dmax was set to 162 Angstroms. GNOM gives a similar Dmax at a qmax of 0.3 A^-1.","experiment_description":null,"tags":[],"intensity_unit":"arbitrary","experimental_mw":141.1,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":null,"porod_mw_error":null,"pddf_i0":null,"pddf_i0_error":null,"guinier_i0":64.3829,"guinier_i0_error":null,"pddf_rg":null,"pddf_rg_error":null,"guinier_rg":4.185,"guinier_rg_error":0.013,"pddf_dmax":null,"pddf_dmax_error":null,"porod_volume":null,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":10,"guinier_point_last":40,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDX48_datloglog_img.png","symmetry":null,"last_modified":"2025-09-22T09:36:25.172022+02:00","bragg_peak":[]}