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.
View the complete summary.json source
{
"code": "SASDUW4",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/A",
"project": {
"title": "Ligand‐induced <scp>CaMKIIα</scp>\n hub Trp403 flip, hub domain stacking, and modulation of kinase activity",
"publication": {
"title": "Ligand‐induced <scp>CaMKIIα</scp>\n hub Trp403 flip, hub domain stacking, and modulation of kinase activity",
"author_list": "Narayanan D, Larsen A, Gauger S, Adafia R, Hammershøi R, Hamborg L, Bruus‐Jensen J, Griem‐Krey N, Gee C, Frølund B, Stratton M, Kuriyan J, Kastrup J, Langkilde A, Wellendorph P, Solbak S",
"journal": "Protein Science",
"doi": "10.1002/pro.5152",
"pmid": null,
"published_date": "2024 Sep 14"
},
"status": "released",
"submitted_date": "2024-03-18",
"released_date": "2024-09-18"
},
"pddf_data": null,
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDUW4.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUW4_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUW4_kratky_img.png",
"pddf_plot": null,
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUW4_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDUW4.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 6M",
"resolution": null
},
"name": "PETRA III",
"city": "DESY; Hamburg",
"country": "Germany",
"beamline_name": "EMBL P12",
"beam_geometry": null,
"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": "Calcium/calmodulin-dependent protein kinase type II subunit alpha",
"short_name": "CaMKIIα WT hub",
"sequence": "GPHMVRKQEIIKVTEQLIEAISNGDFESYTKMCDPGMTAFEPEALGNLVEGLDFHRFYFENLWSRNSKPVHTTILNPHIHLMGDESACIAYIRITQYLDAGGIPRTAQSEETRVWHRRDGKWQIVHFHRSGAPSV",
"organism": "Homo sapiens",
"uniprot_code": "Q9UQM7",
"uniprot_range_first": 345,
"uniprot_range_last": 475,
"oligomerization": "dodecamer",
"molecular_type": "protein",
"uniprot_sequence": "MATITCTRFTEEYQLFEELGKGAFSVVRRCVKVLAGQEYAAKIINTKKLSARDHQKLERE\nARICRLLKHPNIVRLHDSISEEGHHYLIFDLVTGGELFEDIVAREYYSEADASHCIQQIL\nEAVLHCHQMGVVHRDLKPENLLLASKLKGAAVKLADFGLAIEVEGEQQAWFGFAGTPGYL\nSPEVLRKDPYGKPVDLWACGVILYILLVGYPPFWDEDQHRLYQQIKAGAYDFPSPEWDTV\nTPEAKDLINKMLTINPSKRITAAEALKHPWISHRSTVASCMHRQETVDCLKKFNARRKLK\nGAILTTMLATRNFSGGKSGGNKKSDGVKESSESTNTTIEDEDTKVRKQEIIKVTEQLIEA\nISNGDFESYTKMCDPGMTAFEPEALGNLVEGLDFHRFYFENLWSRNSKPVHTTILNPHIH\nLMGDESACIAYIRITQYLDAGGIPRTAQSEETRVWHRRDGKWQIVHFHRSGAPSVLPH",
"mw": 15.477,
"total_mw": 185.724,
"number_molecules": 12,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "The protein construct used for SAXS contains an additional four non-native amino acids at the N-terminus (GPHM)."
},
{
"long_name": "2-(6-(4-chlorophenyl)imidazo[1,2-b]pyridazine-2-yl)acetic acid",
"short_name": "PIPA",
"sequence": null,
"organism": null,
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "other",
"uniprot_sequence": "",
"mw": 0.3,
"total_mw": 0.3,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": ""
}
],
"buffer": {
"name": "20 mM MES, 150 mM NaCl, 1 mM DTT, 200 µM PIPA",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 6.0,
"deuteration": null
},
"purity_method": null,
"name": "Calcium/calmodulin-dependent protein kinase type II alpha (CaMKIIα) WT hub domain with PIPA (iv)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Copenhagen, Denmark",
"full_name": "University of Copenhagen",
"webpage": "http://www.ku.dk/"
}
],
"contributor_name": "Annette",
"contributor_surname": "Langkilde",
"orcid": ""
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2023-03-17",
"storage_temperature": 10.0,
"cell_temperature": 20.0,
"exposure_time": 0.095,
"number_of_frames": 30,
"wavelength": 0.124,
"sample_detector_distance": 3.0,
"concentration_min": null,
"concentration_max": 2.3,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.038,
"s_max": 4.47,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDUW4_fit1_model1_img.png",
"software": "PyMOL",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDUW4_fit1_model1.pdb",
"model_mw": 178.6,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "Dodecameric model based on pdb entry 5ig3",
"user": 42
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDUW4_fit1_model2_img.png",
"software": "PyMOL",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDUW4_fit1_model2.pdb",
"model_mw": 357.2,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "\"d2\" corresponding to two stacked dodecamers",
"user": 42
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDUW4_fit1_fixed_fit_img.png",
"software": "OLIGOMER",
"chi_square_value": 2.32,
"p_value": 0.0,
"fit_residual_plot": "SASDUW4_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDUW4_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/oligomer_51IbPs1.log",
"software_version": null,
"description": "The input for OLIOGMER consisted of CaMKIIa WT hub dodecamer model (based on PDB entry 5ig3) and multimers of self-associated (stacked) dodecamers ranging from two dodecamers to 40. (1-16,20,24,32,40 dodecamers, respectively)."
}
],
"estimated_volume_method": null,
"pddf_software": null,
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": "Several samples of CaMKIIa WT hub with PIPA were collected. This is sample (iv) - supernatant after centrifugation. The sample is not monodisperse but fitting attempted by a mixture of CaMKIIa WT hub dodecamers and multimers of self-associated (stacked) dodecamers. Only single and double dodecameric models are shown.",
"experiment_description": "Synchrotron SAXS data from solutions of calcium/calmodulin-dependent protein kinase type II alpha (CaMKIIα) WT hub domain with PIPA in 20 mM MES, 150 mM NaCl, 1 mM DTT, 200 µM PIPA, pH 6 were collected on the EMBL P12 beam line at PETRA III (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 2.30 mg/ml was measured at 20°C. 30 successive 0.095 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.",
"tags": [],
"intensity_unit": "1/cm",
"experimental_mw": 715.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": null,
"pddf_i0_error": null,
"guinier_i0": 0.680757,
"guinier_i0_error": null,
"pddf_rg": null,
"pddf_rg_error": null,
"guinier_rg": 15.6,
"guinier_rg_error": 2.364,
"pddf_dmax": 90.0,
"pddf_dmax_error": null,
"porod_volume": null,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 5,
"guinier_point_last": 13,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDUW4_datloglog_img.png",
"symmetry": null,
"last_modified": "2024-09-18T12:55:01.492513+02:00",
"bragg_peak": []
}
