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": "SASDF73",
"status": "Published",
"type_of_curve": "Single concentration",
"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/SASDF73.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDF73.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF73_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF73_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDF73_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF73_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDF73.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 - Src homology 3-2 kinase domain",
"short_name": "hBTK - SH3-SH2-KD",
"sequence": "GAMGSMSELKKVVALYDYMPMNANDLQLRKGDEYFILEESNLPWWRARDKNGQEGYIPSNYVTEAEDSIEMYEWYSKHMTRSQAEQLLKQEGKEGGFIVRDSSKAGKYTVSVFAKSTGDPQGVIRHYVVCSTPQSQYYLAEKHLFSTIPELINYHQHNSAGLISRLKYPVSQQNKNAPSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES",
"organism": "Homo sapiens",
"uniprot_code": "Q06187",
"uniprot_range_first": 214,
"uniprot_range_last": 659,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MAAVILESIFLKRSQQKKKTSPLNFKKRLFLLTVHKLSYYEYDFERGRRGSKKGSIDVEK\nITCVETVVPEKNPPPERQIPRRGEESSEMEQISIIERFPYPFQVVYDEGPLYVFSPTEEL\nRKRWIHQLKNVIRYNSDLVQKYHPCFWIDGQYLCCSQTAKNAMGCQILENRNGSLKPGSS\nHRKTKKPLPPTPEEDQILKKPLPPEPAAAPVSTSELKKVVALYDYMPMNANDLQLRKGDE\nYFILEESNLPWWRARDKNGQEGYIPSNYVTEAEDSIEMYEWYSKHMTRSQAEQLLKQEGK\nEGGFIVRDSSKAGKYTVSVFAKSTGDPQGVIRHYVVCSTPQSQYYLAEKHLFSTIPELIN\nYHQHNSAGLISRLKYPVSQQNKNAPSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGK\nWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANG\nCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDF\nGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYER\nFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES",
"mw": 52.171,
"total_mw": 52.171,
"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 - SH3-SH2-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": "2018-11-02",
"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": null,
"concentration_max": 4.32,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.04,
"s_max": 4.946,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF73_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/SASDF73_fit1_model1.pdb",
"model_mw": 41.676,
"bead_radius": 2.1,
"log": "https://www.sasbdb.org/media/log_files/BTK_3-2-KD_DAMMIN.log",
"symmetry": null,
"comment": null,
"user": 406
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF73_fit1_fixed_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 0.937,
"p_value": 0.139358,
"fit_residual_plot": "SASDF73_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF73_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/BTK_3-2-KD_DAMMIN.log",
"software_version": null,
"description": "Ab initio bead model generated by DAMMIN for Bruton's tyrosine kinase SH3-SH2-KD autoinhibited module."
},
{
"models": [],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF73_fit2_fixed_fit_img.png",
"software": "EOM/GAJOE",
"chi_square_value": 0.847,
"p_value": 0.221364,
"fit_residual_plot": "SASDF73_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF73_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Btk-3-2-KD_EOM_fFWyjXo.log",
"software_version": null,
"description": "EOM analysis of human Btk Sh3-SH2-KD using using high resolution structures of SH3, SH2 and kinase domains (PDB 1QLY, 2GE9 and 1K2P)."
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF73_fit3_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "4x12",
"ext_code": "4X12",
"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/SASDF73_fit3_model1.pdb",
"model_mw": 48.13,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/Btk_3-2-KD_CRYSOL_yUQEhve.log",
"symmetry": null,
"comment": null,
"user": 406
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF73_fit3_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.559,
"p_value": 0.0,
"fit_residual_plot": "SASDF73_fit3_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF73_fit3.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Btk_3-2-KD_CRYSOL_dVc6rNi.log",
"software_version": null,
"description": "CRYSOL fitting to crystal structure of mouse Btk SH3-SH2-KD autoinhibiteed module (PDB 4XI2)."
}
],
"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 auto-inhibited module SH3-SH2-kinase domain (amino acids 214-659) 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 0.78 and 4.32 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 raw curve measured from highest concentration was used for further analysis. The final scattering curve was analysed using PRIMUS software (ATSAS). The model depicts the DAMMIN ab initio reconstruction superimposed with the crystal structure 4XI2 (PDB). Ensemble optimisation method (EOM) was performed using three domains structure (1QLY, 2GE9 and 1K2P, PDB) to assess construct’s flexibility.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 45.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 45.0,
"porod_mw_error": null,
"pddf_i0": 44.18,
"pddf_i0_error": null,
"guinier_i0": 44.28,
"guinier_i0_error": 0.07,
"pddf_rg": 2.62,
"pddf_rg_error": null,
"guinier_rg": 2.62,
"guinier_rg_error": 0.01,
"pddf_dmax": 8.3,
"pddf_dmax_error": null,
"porod_volume": 72.26,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 18,
"guinier_point_last": 98,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDF73_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-08-28T15:27:50.651789+02:00",
"bragg_peak": []
}
