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{
"code": "SASDF53",
"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/SASDF53.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDF53.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF53_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF53_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDF53_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF53_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDF53.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, kinase domain",
"short_name": "Btk-KD",
"sequence": "GAMGSGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES",
"organism": "Homo sapiens",
"uniprot_code": "Q06187",
"uniprot_range_first": 391,
"uniprot_range_last": 659,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MAAVILESIFLKRSQQKKKTSPLNFKKRLFLLTVHKLSYYEYDFERGRRGSKKGSIDVEK\nITCVETVVPEKNPPPERQIPRRGEESSEMEQISIIERFPYPFQVVYDEGPLYVFSPTEEL\nRKRWIHQLKNVIRYNSDLVQKYHPCFWIDGQYLCCSQTAKNAMGCQILENRNGSLKPGSS\nHRKTKKPLPPTPEEDQILKKPLPPEPAAAPVSTSELKKVVALYDYMPMNANDLQLRKGDE\nYFILEESNLPWWRARDKNGQEGYIPSNYVTEAEDSIEMYEWYSKHMTRSQAEQLLKQEGK\nEGGFIVRDSSKAGKYTVSVFAKSTGDPQGVIRHYVVCSTPQSQYYLAEKHLFSTIPELIN\nYHQHNSAGLISRLKYPVSQQNKNAPSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGK\nWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANG\nCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDF\nGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYER\nFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES",
"mw": 31.793,
"total_mw": 31.793,
"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 - kinase domain",
"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": "2018-05-11",
"storage_temperature": 10.0,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 10,
"wavelength": 0.09919,
"sample_detector_distance": 2.869,
"concentration_min": 0.91,
"concentration_max": 4.15,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.058,
"s_max": 4.928,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF53_fit1_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/SASDF53_fit1_model1.pdb",
"model_mw": 25.418,
"bead_radius": 1.7,
"log": "https://www.sasbdb.org/media/log_files/Btk_KD_DAMMIN.log",
"symmetry": "P1",
"comment": null,
"user": 406
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF53_fit1_fixed_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 1.002,
"p_value": 0.092064,
"fit_residual_plot": "SASDF53_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF53_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Btk_KD_DAMMIN.log",
"software_version": null,
"description": "Bruton's tyrosine kinase - kinase domain ab initio bead model generated by DAMMIN (Online ATSAS)"
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF53_fit2_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "1k2p",
"ext_code": "1K2P",
"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/SASDF53_fit2_model1.pdb",
"model_mw": 29.73,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/CRYSOL_1k2p.log",
"symmetry": null,
"comment": null,
"user": 406
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF53_fit2_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.275,
"p_value": 0.0,
"fit_residual_plot": "SASDF53_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF53_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/CRYSOL_1k2p.log",
"software_version": null,
"description": "CRYSOL fitting to PDB 1k2p crystal structure."
}
],
"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 kinase domain (amino acids 391-659) 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 0.91 and 4.15 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 crystal structure 1K2P (PDB).",
"tags": [],
"intensity_unit": null,
"experimental_mw": 28.9,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 30.0,
"porod_mw_error": null,
"pddf_i0": 24.94,
"pddf_i0_error": null,
"guinier_i0": 24.98,
"guinier_i0_error": 0.034,
"pddf_rg": 2.096,
"pddf_rg_error": null,
"guinier_rg": 2.09,
"guinier_rg_error": 0.02,
"pddf_dmax": 6.75,
"pddf_dmax_error": null,
"porod_volume": 52.07,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 3,
"guinier_point_last": 120,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDF53_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-01-08T13:58:38.363103+01:00",
"bragg_peak": []
}
