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{
"code": "SASDUV4",
"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/SASDUV4.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUV4_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUV4_kratky_img.png",
"pddf_plot": null,
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUV4_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDUV4.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "pixel counting",
"name": "Pilatus3 R 300K",
"resolution": 172.0
},
"name": "University of Copenhagen, Department of Drug Design and Pharmacology",
"city": "Copenhagen",
"country": "Denmark",
"beamline_name": "Xenocs BioXolver L with MetalJet",
"beam_geometry": null,
"type_of_source": "X-ray in house",
"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 (iii)",
"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": "2023-05-30",
"storage_temperature": 10.0,
"cell_temperature": 25.0,
"exposure_time": 60.0,
"number_of_frames": 40,
"wavelength": 0.13402,
"sample_detector_distance": 0.6325,
"concentration_min": null,
"concentration_max": 3.9,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.171,
"s_max": 5.082,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDUV4_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/SASDUV4_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/SASDUV4_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/SASDUV4_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/SASDUV4_fit1_fixed_fit_img.png",
"software": "OLIGOMER",
"chi_square_value": 5.6,
"p_value": 0.0,
"fit_residual_plot": "SASDUV4_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDUV4_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/oligomer_ydip3vV.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 (iii). 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": "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 using a Xenocs BioXolver L with MetalJet (University of Copenhagen, Department of Drug Design and Pharmacology) equipped with a Pilatus3 R 300K detector at a sample-detector distance of 0.6 m and at a wavelength of λ = 0.13402 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.90 mg/ml was measured at 25°C. 40 successive 60 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": "arbitrary",
"experimental_mw": 650.0,
"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": 0.208923,
"guinier_i0_error": null,
"pddf_rg": null,
"pddf_rg_error": null,
"guinier_rg": 4.464,
"guinier_rg_error": 0.625,
"pddf_dmax": 17.0,
"pddf_dmax_error": null,
"porod_volume": 556.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 6,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDUV4_datloglog_img.png",
"symmetry": null,
"last_modified": "2024-09-18T12:54:56.214364+02:00",
"bragg_peak": []
}
