{ "code": "SASDDS4", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/A", "project": { "title": "An N-terminally truncated form of cyclic GMP-dependent protein kinase Iα (PKG Iα) is monomeric and autoinhibited and provides a model for activation.", "publication": { "title": "An N-terminally truncated form of cyclic GMP-dependent protein kinase Iα (PKG Iα) is monomeric and autoinhibited and provides a model for activation.", "author_list": "Moon TM, Sheehe JL, Nukareddy P, Nausch LW, Wohlfahrt J, Matthews DE, Blumenthal DK, Dostmann WR", "journal": "J Biol Chem", "doi": "10.1074/jbc.RA117.000647", "pmid": "29602907", "published_date": "2018 May 25" }, "status": "released", "submitted_date": "2018-03-02", "released_date": "2018-03-28" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDS4.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDS4.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDS4_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDS4_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDS4_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDS4_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDS4.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Rayonix MX225-HE", "resolution": null }, "name": "Stanford Synchrotron Radiation Lightsource (SSRL)", "city": "Menlo Park, CA", "country": "USA", "beamline_name": "BL4-2", "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": "cGMP-dependent protein kinase 1", "short_name": "∆53 PKG Iα", "sequence": "GAMDIGPRTTRAQGISAEPQTYRSFHDLRQAFRKFTKSERSKDLIKEAILDNDFMKNLELSQIQEIVDCMYPVEYGKDSCIIKEGDVGSLVYVMEDGKVEVTKEGVKLCTMGPGKVFGELAILYNCTRTATVKTLVNVKLWAIDRQCFQTIMMRTGLIKHTEYMEFLKSVPTFQSLPEEILSKLADVLEETHYENGEYIIRQGARGDTFFIISKGKVNVTREDSPNEDPVFLRTLGKGDWFGEKALQGEDVRTANVIAAEAVTCLVIDRDSFKHLIGGLDDVSNKAYEDAEAKAKYEAEAAFFANLKLSDFNIIDTLGVGGFGRVELVQLKSEESKTFAMKILKKRHIVDTRQQEHIRSEKQIMQGAHSDFIVRLYRTFKDSKYLYMLMEACLGGELWTILRDRGSFEDSTTRFYTACVVEAFAYLHSKGIIYRDLKPENLILDHRGYAKLVDFGFAKKIGFGKKTWTFCGTPEYVAPEIILNKGHDISADYWSLGILMYELLTGSPPFSGPDPMKTYNIILRGIDMIEFPKKIAKNAANLIKKLCRDNPSERLGNLKNGVKDIQKHKWFEGFNWEGLRKGTLTPPIIPSVASPTDTSNFDSFPEDNDEPPPDDNSGWDIDF", "organism": "Bos taurus", "uniprot_code": "P00516", "uniprot_range_first": 54, "uniprot_range_last": 671, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MSELEEDFAKILMLKEERIKELEKRLSEKEEEIQELKRKLHKCQSVLPVPSTHIGPRTTR\nAQGISAEPQTYRSFHDLRQAFRKFTKSERSKDLIKEAILDNDFMKNLELSQIQEIVDCMY\nPVEYGKDSCIIKEGDVGSLVYVMEDGKVEVTKEGVKLCTMGPGKVFGELAILYNCTRTAT\nVKTLVNVKLWAIDRQCFQTIMMRTGLIKHTEYMEFLKSVPTFQSLPEEILSKLADVLEET\nHYENGEYIIRQGARGDTFFIISKGKVNVTREDSPNEDPVFLRTLGKGDWFGEKALQGEDV\nRTANVIAAEAVTCLVIDRDSFKHLIGGLDDVSNKAYEDAEAKAKYEAEAAFFANLKLSDF\nNIIDTLGVGGFGRVELVQLKSEESKTFAMKILKKRHIVDTRQQEHIRSEKQIMQGAHSDF\nIVRLYRTFKDSKYLYMLMEACLGGELWTILRDRGSFEDSTTRFYTACVVEAFAYLHSKGI\nIYRDLKPENLILDHRGYAKLVDFGFAKKIGFGKKTWTFCGTPEYVAPEIILNKGHDISAD\nYWSLGILMYELLTGSPPFSGPDPMKTYNIILRGIDMIEFPKKIAKNAANLIKKLCRDNPS\nERLGNLKNGVKDIQKHKWFEGFNWEGLRKGTLTPPIIPSVASPTDTSNFDSFPEDNDEPP\nPDDNSGWDIDF", "mw": 70.433, "total_mw": 70.433, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50 mM MES, 300 mM NaCl, 1 mM TCEP, 5 mM DTT", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 6.9, "deuteration": null }, "purity_method": null, "name": "cGMP-dependent protein kinase 1: ∆53 PKG Iα", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Tucson, AZ, USA", "full_name": "University of Arizona", "webpage": "http://www.arizona.edu/" } ], "contributor_name": "Thomas", "contributor_surname": "Moon", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2015-06-06", "storage_temperature": 4.0, "cell_temperature": 22.0, "exposure_time": 1.0, "number_of_frames": 600, "wavelength": 0.1127, "sample_detector_distance": 1.7, "concentration_min": null, "concentration_max": null, "sample_volume": null, "flow_rate": null, "s_min": 0.087, "s_max": 5.136, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDS4_fit1_model1_img.png", "software": "DAMFILT", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "5.0", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDDS4_fit1_model1.pdb", "model_mw": 73.548, "bead_radius": 3.25, "log": null, "symmetry": "p1", "comment": "Filtered, Averaged 3-D envelope", "user": 268 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDS4_fit1_fit_img.png", "software": "DAMMIN", "chi_square_value": 0.602, "p_value": 0.999, "fit_residual_plot": "SASDDS4_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDS4_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/DAMMINon_102.log", "software_version": "online", "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of cGMP-dependent protein kinase 1 (∆53 PKG Iα) were collected using SEC-SAXS on the BL4-2 beam line at the Stanford Synchrotron Radiation Lightsource (SSRL; Stanford, CA, USA) using a Rayonix MX225-HE detector at a sample-detector distance of 1.7 m and at a wavelength of λ = 0.1127 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). A 35 μL sample of 6 mg/mL PKG Iα ∆53 was injected onto a Superdex 200 3.2/30 column (GE) and eluted isocratically using an Ettan FPLC (GE) at 0.05 mL/min in 50 mM MES, 300 mM NaCl, 1mM TCEP, pH 6.9 supplemented with 5 mM DTT as a radical scavenger. The eluant stream was connected in-line to a 1.5 mm quartz capillary. Data were collected with a 1 second/frame exposure rate at 22°C. A total of 600 frames were collected. Frames 410-459 containing the peak corresponding to ∆53 PKG were averaged and subtracted from background. The scattering curve, Guinier and P(r) functions, and Porod volume were calculated using the PRIMUS (ATSAS) program suite.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 70.433, "experimental_mw_error": null, "guinier_i0_mw": 75.814, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 323.9, "pddf_i0_error": 1.8, "guinier_i0": 321.37, "guinier_i0_error": 2.21, "pddf_rg": 3.02, "pddf_rg_error": 0.03, "guinier_rg": 2.971, "guinier_rg_error": 0.031, "pddf_dmax": 9.68, "pddf_dmax_error": null, "porod_volume": 105.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 10, "guinier_point_last": 39, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDDS4_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }