The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
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{
"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": []
}
