{"code":"SASDVY5","status":"Published","type_of_curve":"SEC-SAS","angular_unit":"1/A","project":{"title":"The Pseudoenzyme β‐Amylase9 From Arabidopsis Activates α‐Amylase3: A Possible Mechanism to Promote Stress‐Induced Starch Degradation","publication":{"title":"The Pseudoenzyme β‐Amylase9 From Arabidopsis Activates α‐Amylase3: A Possible Mechanism to Promote Stress‐Induced Starch Degradation","author_list":"Berndsen C, Storm A, Sardelli A, Hossain S, Clermont K, McFather L, Connor M, Monroe J","journal":"Proteins: Structure, Function, and Bioinformatics","doi":"10.1002/prot.26803","pmid":null,"published_date":"2025 Jan 23"},"status":"released","submitted_date":"2024-07-30","released_date":"2025-01-20"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDVY5.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDVY5.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVY5_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVY5_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVY5_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVY5_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDVY5.sascif","experiment":{"instrument":{"detector":{"type":null,"name":"Pilatus3 X 2M","resolution":172.0},"name":"Advanced Light Source (ALS)","city":"Berkeley, CA","country":"USA","beamline_name":"12.3.1 (SIBYLS)","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":"Inactive beta-amylase 9","short_name":"BAM9","sequence":"PFLKSTPKSKSLESVKLFVGLPLDTVSDCNNVNHLKAITAGLKALKLLGVEGIELPIFWGVVEKEAAGKYEWSGYLAVAEIVKKVGLKLHASLSFHGSKQTEIGLPDWVAKIGDAEPGIYFTDRYGQQYKDCLSFAVDDVPVLDGKTPMEVYRGFCESFKSAFADYMGNTITGITLGLGPDGELKYPSHQHNAKLSGAGEFQCYDKHMLSALKGYAESTGNPLWGLGGPHDAPAYDQQPNSSSFFSDGGSWESQYGDFFLSWYSSLLTSHADRVLSVASSAFSGIGVPLCGKLPLLHQWHKLRSHPSELTAGFYSSNGQDRYEAIAEIFAKNSCRMIIPGMDLSDEHQSPESLSSPESLLGHIKTSCKKQGVVVSGQNSSTPVPGGFERIVENLKDENVGIDLFTYQRMGALFFSPEHFHAFTVFVRNLSQFELSSDDQASEAEVEAETASIGSGTGAPSLQTA","organism":"Arabidopsis thaliana","uniprot_code":"Q8VYW2","uniprot_range_first":73,"uniprot_range_last":536,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MEVSVIGNPQARICRAELAYRELGFRFGSDVISGESRNRVSFCNQSSKWKEIAIRCSSRS\nVKCEAIVSDDASPFLKSTPKSKSLESVKLFVGLPLDTVSDCNNVNHLKAITAGLKALKLL\nGVEGIELPIFWGVVEKEAAGKYEWSGYLAVAEIVKKVGLKLHASLSFHGSKQTEIGLPDW\nVAKIGDAEPGIYFTDRYGQQYKDCLSFAVDDVPVLDGKTPMEVYRGFCESFKSAFADYMG\nNTITGITLGLGPDGELKYPSHQHNAKLSGAGEFQCYDKHMLSALKGYAESTGNPLWGLGG\nPHDAPAYDQQPNSSSFFSDGGSWESQYGDFFLSWYSSLLTSHADRVLSVASSAFSGIGVP\nLCGKLPLLHQWHKLRSHPSELTAGFYSSNGQDRYEAIAEIFAKNSCRMIIPGMDLSDEHQ\nSPESLSSPESLLGHIKTSCKKQGVVVSGQNSSTPVPGGFERIVENLKDENVGIDLFTYQR\nMGALFFSPEHFHAFTVFVRNLSQFELSSDDQASEAEVEAETASIGSGTGAPSLQTA","mw":50.296,"total_mw":50.296,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":"BAM9 expressed from a pETDeut-1 vector"},{"long_name":"Alpha-amylase 3, chloroplastic","short_name":"AMY3","sequence":"MNKSPVAIRATSSDTAVVETAQSDDVIFKEIFPVQRIEKAEGKIYVRLKEVKEKNWELSVGCSIPGKWILHWGVSYVGDTGSEWDQPPEDMRPPGSIAIKDYAIETPLKKLSEGDSFFEVAINLNLESSVAALNFVLKDEETGAWYQHKGRDFKVPLVDDVPDNGNLIGAKKGFGALGQLSNIPLKQDKSSAETDSIEERKGLQEFYEEMPISKRVADDNSVSVTARKCPETSKNIVSIETDLPGDVTVHWGVCKNGTKKWEIPSEPYPEETSLFKNKALRTRLQRKDDGNGSFGLFSLDGKLEGLCFVLKLNENTWLNYRGEDFYVPFLTSSSSPVETEAAQVSKPKRKTDKEVSASGFTKEIITEIRNLAIDISSHKNQKTNVKEVQENILQEIEKLAAEAYSIFRSTTPAFSEEGVLEAEADKPDIKISSGTGSGFEILCQGFNWESNKSGRWYLELQEKADELASLGFTVLWLPPPTESVSPEGYMPKDLYNLNSRYGTIDELKDTVKKFHKVGIKVLGDAVLNHRCAHFKNQNGVWNLFGGRLNWDDRAVVADDPHFQGRGNKSSGDNFHAAPNIDHSQDFVRKDIKEWLCWMMEEVGYDGWRLDFVRGFWGGYVKDYMDASKPYFAVGEYWDSLSYTYGEMDYNQDAHRQRIVDWINATSGAAGAFDVTTKGILHTALQKCEYWRLSDPKGKPPGVVGWWPSRAVTFIENHDTGSTQGHWRFPEGKEMQGYAYILTHPGTPAVFFDHIFSDYHSEIAALLSLRNRQKLHCRSEVNIDKSERDVYAAIIDEKVAMKIGPGHYEPPNGSQNWSVAVEGRDYKVWETS","organism":"Arabidopsis thaliana","uniprot_code":"Q94A41","uniprot_range_first":57,"uniprot_range_last":887,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MSTVPIESLLHHSYLRHNSKVNRGNRSFIPISLNLRSHFTSNKLLHSIGKSVGVSSMNKS\nPVAIRATSSDTAVVETAQSDDVIFKEIFPVQRIEKAEGKIYVRLKEVKEKNWELSVGCSI\nPGKWILHWGVSYVGDTGSEWDQPPEDMRPPGSIAIKDYAIETPLKKLSEGDSFFEVAINL\nNLESSVAALNFVLKDEETGAWYQHKGRDFKVPLVDDVPDNGNLIGAKKGFGALGQLSNIP\nLKQDKSSAETDSIEERKGLQEFYEEMPISKRVADDNSVSVTARKCPETSKNIVSIETDLP\nGDVTVHWGVCKNGTKKWEIPSEPYPEETSLFKNKALRTRLQRKDDGNGSFGLFSLDGKLE\nGLCFVLKLNENTWLNYRGEDFYVPFLTSSSSPVETEAAQVSKPKRKTDKEVSASGFTKEI\nITEIRNLAIDISSHKNQKTNVKEVQENILQEIEKLAAEAYSIFRSTTPAFSEEGVLEAEA\nDKPDIKISSGTGSGFEILCQGFNWESNKSGRWYLELQEKADELASLGFTVLWLPPPTESV\nSPEGYMPKDLYNLNSRYGTIDELKDTVKKFHKVGIKVLGDAVLNHRCAHFKNQNGVWNLF\nGGRLNWDDRAVVADDPHFQGRGNKSSGDNFHAAPNIDHSQDFVRKDIKEWLCWMMEEVGY\nDGWRLDFVRGFWGGYVKDYMDASKPYFAVGEYWDSLSYTYGEMDYNQDAHRQRIVDWINA\nTSGAAGAFDVTTKGILHTALQKCEYWRLSDPKGKPPGVVGWWPSRAVTFIENHDTGSTQG\nHWRFPEGKEMQGYAYILTHPGTPAVFFDHIFSDYHSEIAALLSLRNRQKLHCRSEVNIDK\nSERDVYAAIIDEKVAMKIGPGHYEPPNGSQNWSVAVEGRDYKVWETS","mw":93.604,"total_mw":93.604,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":""}],"buffer":{"name":"20 mM HEPES, 100 mM NaCl, 0.2 mM TCEP","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":7.0,"deuteration":null},"purity_method":null,"name":"pseudoamylase BAM9 bound to alpha-amylase AMY3","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":null,"address":"Harrisonburg, Virginia, USA","full_name":"James Madison University","webpage":"https://www.jmu.edu/"}],"contributor_name":"Christopher","contributor_surname":"Berndsen","orcid":"https://orcid.org/0000-0002-4285-4341"}],"concentration_method":null,"concentration_unit":null,"date":"2023-05-16","storage_temperature":-80.0,"cell_temperature":10.0,"exposure_time":2.0,"number_of_frames":20,"wavelength":0.1027,"sample_detector_distance":2.1,"concentration_min":null,"concentration_max":4.0,"sample_volume":null,"flow_rate":null,"s_min":0.114,"s_max":4.729,"total_exposure_time":null,"seccolumn":40},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDVY5_fit1_model1_img.png","software":"BILBOMD","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDVY5_fit1_model1.pdb","model_mw":146.8,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":394}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVY5_fit1_fitfoxs_img.png","software":"FoXS","chi_square_value":1.405163,"p_value":0.0,"fit_residual_plot":"SASDVY5_fit1_fitfoxsresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDVY5_fit1.dat","fit_log":null,"software_version":null,"description":""}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"5.0","i0_calibration_standard":null,"description":"Purified protein samples of AMY3 and BAM9 combined were shipped overnight at 4°C and analyzed using SEC-SAXS with in-line with UV/vis absorbance at 280nm and Multi-angle light scattering (MALS). Radially averaged SAXS data files were processed and analyzed in Scatter IV and RAW (Hopkins, 2024).","experiment_description":"Synchrotron SAXS data from solutions of pseudoamylase BAM9 bound to alpha-amylase AMY3 in 20 mM HEPES, 100 mM NaCl, 0.2 mM TCEP, pH 7 were collected on the 12.3.1 (SIBYLS) beam line at the Advanced Light Source (ALS; Berkeley, CA, USA) using a Pilatus3 X 2M detector at a sample-detector distance of 2.1 m and at a wavelength of λ = 0.1027 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A sample at 4 mg/ml was injected onto a Shodex KW-803 column at 10°C. 20 successive 2 second frames were collected through the sample elution peak. 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":146.8,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":200.0,"porod_mw_error":null,"pddf_i0":89.99,"pddf_i0_error":1.48,"guinier_i0":77.6681,"guinier_i0_error":null,"pddf_rg":6.52,"pddf_rg_error":0.11,"guinier_rg":5.047,"guinier_rg_error":1.431,"pddf_dmax":25.5,"pddf_dmax_error":null,"porod_volume":379.7,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":3,"guinier_point_last":24,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDVY5_datloglog_img.png","symmetry":null,"last_modified":"2025-01-23T14:23:02.048022+01:00","bragg_peak":[]}