{ "code": "SASDVX5", "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/SASDVX5.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVX5.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVX5_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVX5_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVX5_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVX5_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVX5.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" } ], "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", "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": 0.5, "s_min": 0.134, "s_max": 4.729, "total_exposure_time": null, "seccolumn": 40 }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVX5_fit1_model1_img.png", "software": "AlphaFold", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "3", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDVX5_fit1_model1.cif", "model_mw": null, "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/SASDVX5_fit1_fixed_fit_img.png", "software": "FoXS", "chi_square_value": 1.024596, "p_value": 0.0, "fit_residual_plot": "SASDVX5_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVX5_fit1.fit", "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": "BAM9 was expressed in BL21 cells with pETDuet-1-BAM9-B cultured with 100 mg/L carbenicillin. Cells were grown to an OD600 of approximately 0.6 at 37° C and 225 rpm, then induced with 1 mM Isopropyl-β-D-thiogalactoside (IPTG) at 20° C overnight. Cells were pelleted, frozen, and then sonicated on ice in 40 ml Buffer A (0.5 M NaCl, 50 mM NaH2PO4, 0.2 mM TCEP, and 2 mM imidazole, pH 8) with an EDTA-free protease-inhibitor tablet (Pierce A32965). Cell debris was removed by centrifugation at 17,000 rcf at 4° C. This supernatant was then diluted to 175 ml with Buffer A. Protein was then purified using an AKTA Start protein purification system with a 1 ml TALON cobalt-affinity column using washes of 2%, 10%, 20%, and 100% Buffer B (Cytiva Life Science, Marlborough, Massachusetts, USA). Buffer B contained 0.5 M NaCl, 50 mM NaH2PO4, 0.2 mM TCEP, and 200 mM imidazole, pH 8. Buffers A and B were supplemented with 3 mM benzamidine (TCI) when purifying AMY3 to reduce degradation. The BAM9 that was analyzed using small-angle X-ray scattering (SAXS) was additionally purified using size exclusion chromatography (SEC) with a Superdex 100 column (Cytiva). Purified protein samples of AMY3 and BAM9 alone and 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. 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 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 at a 0.50 ml/min flow rate 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": 42.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 46.0, "porod_mw_error": null, "pddf_i0": 40.46, "pddf_i0_error": 0.013, "guinier_i0": 40.4915, "guinier_i0_error": null, "pddf_rg": 2.46, "pddf_rg_error": 0.01, "guinier_rg": 2.436, "guinier_rg_error": 0.41, "pddf_dmax": 8.7, "pddf_dmax_error": null, "porod_volume": 86.7, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 6, "guinier_point_last": 46, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDVX5_datloglog_img.png", "symmetry": null, "last_modified": "2025-01-23T14:23:01.159580+01:00", "bragg_peak": [] }