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{
"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": []
}
