{ "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": [] }