The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
Every source field is expanded here, including empty values, list members and fields already shown above.
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{
"code": "SASDF83",
"status": "Published",
"type_of_curve": "Merged",
"angular_unit": "1/nm",
"project": {
"title": "Btk SH2-kinase interface is critical for allosteric kinase activation and its targeting inhibits B-cell neoplasms",
"publication": {
"title": "Btk SH2-kinase interface is critical for allosteric kinase activation and its targeting inhibits B-cell neoplasms",
"author_list": "Duarte D, Lamontanara A, La Sala G, Jeong S, Sohn Y, Panjkovich A, Georgeon S, Kükenshöner T, Marcaida M, Pojer F, De Vivo M, Svergun D, Kim H, Dal Peraro M, Hantschel O",
"journal": "Nature Communications",
"doi": "10.1038/s41467-020-16128-5",
"pmid": null,
"published_date": "2020 May 8"
},
"status": "released",
"submitted_date": "2019-02-20",
"released_date": "2020-01-08"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDF83.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDF83.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF83_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF83_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDF83_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF83_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDF83.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "Dectris",
"name": "Pilatus 1M",
"resolution": 172.0
},
"name": "ESRF",
"city": "Grenoble",
"country": "France",
"beamline_name": "BM29",
"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": "Bruton's tyrosine kinase - full length",
"short_name": "hBTK - FL",
"sequence": "GAMGSMAAVILESIFLKRSQQKKKTSPLNFKKRLFLLTVHKLSYYEYDFERGRRGSKKGSIDVEKITCVETVVPEKNPPPERQIPRRGEESSEMEQISIIERFPYPFQVVYDEGPLYVFSPTEELRKRWIHQLKNVIRYNSDLVQKYHPCFWIDGQYLCCSQTAKNAMGCQILENRNGSLKPGSSHRKTKKPLPPTPEEDQILKKPLPPEPAAAPVSTSELKKVVALYDYMPMNANDLQLRKGDEYFILEESNLPWWRARDKNGQEGYIPSNYVTEAEDSIEMYEWYSKHMTRSQAEQLLKQEGKEGGFIVRDSSKAGKYTVSVFAKSTGDPQGVIRHYVVCSTPQSQYYLAEKHLFSTIPELINYHQHNSAGLISRLKYPVSQQNKNAPSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES",
"organism": "Homo sapiens",
"uniprot_code": "Q06187",
"uniprot_range_first": 1,
"uniprot_range_last": 659,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MAAVILESIFLKRSQQKKKTSPLNFKKRLFLLTVHKLSYYEYDFERGRRGSKKGSIDVEK\nITCVETVVPEKNPPPERQIPRRGEESSEMEQISIIERFPYPFQVVYDEGPLYVFSPTEEL\nRKRWIHQLKNVIRYNSDLVQKYHPCFWIDGQYLCCSQTAKNAMGCQILENRNGSLKPGSS\nHRKTKKPLPPTPEEDQILKKPLPPEPAAAPVSTSELKKVVALYDYMPMNANDLQLRKGDE\nYFILEESNLPWWRARDKNGQEGYIPSNYVTEAEDSIEMYEWYSKHMTRSQAEQLLKQEGK\nEGGFIVRDSSKAGKYTVSVFAKSTGDPQGVIRHYVVCSTPQSQYYLAEKHLFSTIPELIN\nYHQHNSAGLISRLKYPVSQQNKNAPSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGK\nWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANG\nCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDF\nGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYER\nFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES",
"mw": 76.684,
"total_mw": 76.684,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20mM Tris, 150mM NaCl, 1mM TCEP, 5% glycerol",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Bruton's Tyrosine Kinase - Full-length",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Switzerland",
"full_name": "École polytechnique fédérale de Lausanne (EPFL)",
"webpage": "https://www.epfl.ch"
}
],
"contributor_name": "Daniel",
"contributor_surname": "Duarte",
"orcid": "https://orcid.org/0000-0001-6730-7582"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2018-11-03",
"storage_temperature": 10.0,
"cell_temperature": 10.0,
"exposure_time": 1.0,
"number_of_frames": 10,
"wavelength": 0.09919,
"sample_detector_distance": 2.869,
"concentration_min": 0.42,
"concentration_max": 5.18,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.082,
"s_max": 4.946,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF83_fit1_fixed_fit_img.png",
"software": "EOM/GAJOE",
"chi_square_value": 1.312,
"p_value": 0.000598,
"fit_residual_plot": "SASDF83_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF83_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Btk_FL_EOM_G49AXBH.log",
"software_version": null,
"description": "EOM analysis of full-length human Btk using high-resolution structures for all four domains (2Z0P, 1QLY, 2GE9, 1K2P)."
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF83_fit2_model1_img.png",
"software": "DAMMIN",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDF83_fit2_model1.pdb",
"model_mw": 71.73,
"bead_radius": 4.0,
"log": "https://www.sasbdb.org/media/log_files/Btk_FL_DAMMIN_5LZhU45.log",
"symmetry": null,
"comment": null,
"user": 406
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF83_fit2_fixed_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 1.414,
"p_value": 0.000303,
"fit_residual_plot": "SASDF83_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF83_fit2.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Btk_FL_DAMMIN_WCKb9Yq.log",
"software_version": null,
"description": "Ab initio bead model reconstruction of human BTK full-length wild-type using DAMMIN."
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF83_fit3_model1_img.png",
"software": "SREFLEX",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDF83_fit3_model1.pdb",
"model_mw": 75.5,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/Btk_FL_SREFLEX_log_8jdCgf5.txt",
"symmetry": null,
"comment": "Best fitting model derived from SASDC52",
"user": 406
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF83_fit3_fixed_fit_img.png",
"software": "SREFLEX",
"chi_square_value": 6.174,
"p_value": 0.0,
"fit_residual_plot": "SASDF83_fit3_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF83_fit3.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Btk_FL_SREFLEX_log_wxXkW7v.txt",
"software_version": null,
"description": "SREFLEX fitting for human Btk full-length using model SASDC52."
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data for full-length (amino acids 1-659) wild-type of human Bruton’s tyrosine kinase (Btk) in 20 mM Tris-HCl, 150 mM NaCl, 5% Glycerol, 1 mM TCEP, pH 7.5 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Dectris Pilatus 1M detector at a sample-detector distance of 2.849 m and at a wavelength of λ = 0.099 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.42 and 5.48 mg/ml were measured at 10°C. 10 successive 0.5 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve. The final scattering curve was analysed using PRIMUS software (ATSAS). The model depicts the DAMMIN ab initio reconstruction superimposed with the atomic model SASDC52 (EMBL, Hamburg) subject to SREFLEX to improve its agreement with experimental data. Ensemble optimisation method (EOM) was performed using all four domains structure (2Z0P, 1QLY, 2GE9 and 1K2P, PDB) to assess construct’s flexibility.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 67.075,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 71.0,
"porod_mw_error": null,
"pddf_i0": 61.31,
"pddf_i0_error": null,
"guinier_i0": 60.23,
"guinier_i0_error": 0.17,
"pddf_rg": 4.339,
"pddf_rg_error": null,
"guinier_rg": 4.04,
"guinier_rg_error": 0.02,
"pddf_dmax": 15.6,
"pddf_dmax_error": null,
"porod_volume": 114.07,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 64,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDF83_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-08-28T15:27:51.495246+02:00",
"bragg_peak": []
}
