{ "code": "SASDXZ7", "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": null, "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDXZ7.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXZ7_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXZ7_kratky_img.png", "pddf_plot": null, "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXZ7_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDXZ7.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": null, "sequence": ">6VU9_1|Chain A|Threonine--tRNA ligase|Stenotrophomonas maltophilia (strain K279a) (522373)\r\nMAHHHHHHMINITLPDGSRREFENPVSVMEVAQSIGAGLAKATIAGAVDGVLVDASDVIDHDASLRIITAKDEEGVEIIRHSCAHLVGHAVKQLYPDVKMVIGPVIAEGFYYDIYSERPFTPDDMAAIEKRMGELIAQDYDVIKKMTPRAEVIEIFKARGEDYKLRLIEDMSEDIQAMGMYYHQEYVDMCRGPHVPNTRFLKAFKLTRISGAYWRGDAQNEQLQRIYGTAWADKKQLEAYIKRIEEAEMRDHRRIGKQQDLFHLQEEAPGLVFWHPKGWALWQVVEQYMRKVYRNSGYGEVRCPQILDVSLWKKSGHWDNYQDNMFFTESEKRTYAVKPMNCPGHIQVFNQGLHSYRDLPIRYGEFGSCHRNEPSGALHGILRVRGFTQDDGHVFCTENQIESEVTAFHQQALAVYQHFGFDEIQIKIALRPESRLGDDATWDKAEGALRSALTACGVEWQELPGEGAFYGPKIEYHLKDAIGRTWQLGTMQVDFMMPGRLGAEYVDENSQKKHPVMLHRAIVGSMERFLGILIEHHAGQFPAWLAPTQVVVANITDAQADYVSGVTKTLAEQGFRVSSDLRNEKIGYKIREHTLQRVPYLLVIGDREKENGAVAVRTRSGEDLGSMSLQAFIERLHAEGA", "organism": "Stenotrophomonas maltophilia (strain K279a) (522373)", "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 I vs q fit is an average of 100 fitted curves for 100 conformations." } ], "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 for open state based on PDB entry 6vu9", "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/SASDXZ7_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/SASDXZ7_fit1_model1.pdb", "model_mw": 146.0, "bead_radius": null, "log": null, "symmetry": null, "comment": "Ensemble structure.", "user": 1185 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDXZ7_fit1_fixed_fit_img.png", "software": "FoXS", "chi_square_value": 1.573482, "p_value": 0.0, "fit_residual_plot": "SASDXZ7_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDXZ7_fit1.fit", "fit_log": null, "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDXZ7_fit2_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/SASDXZ7_fit2_model1.pdb", "model_mw": 146.0, "bead_radius": null, "log": null, "symmetry": null, "comment": "Best fitting structure for 6VU9-like state.", "user": 1185 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDXZ7_fit2_fixed_fit_img.png", "software": "FoXS", "chi_square_value": 1.445178, "p_value": 0.0, "fit_residual_plot": "SASDXZ7_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDXZ7_fit2.fit", "fit_log": null, "software_version": null, "description": "Best fit in the ensemble." } ], "estimated_volume_method": null, "pddf_software": "BioXTAS RAW", "pddf_software_version": "2.3.0", "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": null, "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": 65.07482, "pddf_i0_error": null, "guinier_i0": 64.3829, "guinier_i0_error": null, "pddf_rg": 4.31, "pddf_rg_error": null, "guinier_rg": 4.185, "guinier_rg_error": 0.013, "pddf_dmax": 16.2, "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": "SASDXZ7_datloglog_img.png", "symmetry": null, "last_modified": "2025-09-22T09:36:24.294614+02:00", "bragg_peak": [] }