{ "code": "SASDXX4", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/A", "project": { "title": "Structural, biophysical and biochemical studies of CAZYmes involved in exopolysaccharides degradation of microbial biofilms", "publication": { "title": "Structural, biophysical and biochemical studies of CAZYmes involved in exopolysaccharides degradation of microbial biofilms", "author_list": "Amanda Freitas Cruz", "journal": "Universidade de São Paulo", "doi": null, "pmid": null, "published_date": "2025 Sep 18" }, "status": "released", "submitted_date": "2025-05-24", "released_date": "2025-11-24" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDXX4.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDXX4.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXX4_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXX4_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDXX4_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXX4_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDXX4.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus3 X 1M", "resolution": 0.172 }, "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": "Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB", "short_name": "Serratia marcescens", "sequence": "CSQADVPRFTPPAERPVGPMERPWPANRYAVLAYHDVEDGAADQRYMSVRTSALNEQFAWLKQNGYQPVSVEQILQAQNGGPALPNKAVLLTFDDGYRSFYSRVFPLLKAYNWPAVLAPVGVWLDAPADKPVDFGGLMTPRDRFLTWQQVREVSDSGLVEIGAHTYASHYGGIANPQGNTEPAVANRLYDAKQGRYESEAEYRQRIEKDVALITQRITAATGKAPRVWVWPYGAAGGVALDIARKHGYRMALTLENGLADVNAPENVPRMLVAGNPSLTSFAQQLTQIQNRQIMRVAHVDLDYLYDPDPQQQAKNLDKLIQRIYDLRINTVFLQAFADPKGDGNVRELYFPNRWLPMKADLFNRVSWQLSSRTGVAVYAWMPVLAFELGSDVPRVQRLDPQNGQLSVDDKQYRRLSPFSPVARQRIGEIYEDLAAHATFKGILFHDDALLSDFEDAGPDAAAAYRQAGFADSVAAIRQDPQAMARWTRFKSRALIEFTQSLTERVRAIRGPQVQTARNIYAMPVLDPASEAWFGQNLADFLQAYDWVAPMAMPLMENVPRADSGRWLDQLVGKVAAYPGALDKTVFELQAVDWRKERRISLDDGQLLAEWMRRLQRNGAQSFGYYPDNFLDDRPKLDAVRPVLSSAWFPLP", "organism": "Serratia marcescens", "uniprot_code": "A0A2V4FWX5", "uniprot_range_first": 18, "uniprot_range_last": 668, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MLIRSSLFVLAALLTTGCSQADVPRFTPPAERPVGPMERPWPANRYAVLAYHDVEDGAAD\nQRYMSVRTSALNEQFAWLKQNGYQPVSVEQILQAQNGGPALPNKAVLLTFDDGYRSFYSR\nVFPLLKAYNWPAVLAPVGVWLDAPADKPVDFGGLMTPRDRFLTWQQVREVSDSGLVEIGA\nHTYASHYGGIANPQGNTEPAVANRLYDAKQGRYESEAEYRQRIEKDVALITQRITAATGK\nAPRVWVWPYGAAGGVALDIARKHGYRMALTLENGLADVNAPENVPRMLVAGNPSLTSFAQ\nQLTQIQNRQIMRVAHVDLDYLYDPDPQQQAKNLDKLIQRIYDLRINTVFLQAFADPKGDG\nNVRELYFPNRWLPMKADLFNRVSWQLSSRTGVAVYAWMPVLAFELGSDVPRVQRLDPQNG\nQLSVDDKQYRRLSPFSPVARQRIGEIYEDLAAHATFKGILFHDDALLSDFEDAGPDAAAA\nYRQAGFADSVAAIRQDPQAMARWTRFKSRALIEFTQSLTERVRAIRGPQVQTARNIYAMP\nVLDPASEAWFGQNLADFLQAYDWVAPMAMPLMENVPRADSGRWLDQLVGKVAAYPGALDK\nTVFELQAVDWRKERRISLDDGQLLAEWMRRLQRNGAQSFGYYPDNFLDDRPKLDAVRPVL\nSSAWFPLP", "mw": 73.292, "total_mw": 73.292, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB" } ], "buffer": { "name": "phosphate-buffered saline", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.4, "deuteration": null }, "purity_method": null, "name": "Serratia marcescens poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "São Paulo, SP, Brazil", "full_name": "Instituto de Física, Universidade de São Paulo", "webpage": "" } ], "contributor_name": "Amanda", "contributor_surname": "Freitas Cruz", "orcid": "" } ], "concentration_method": null, "concentration_unit": null, "date": "2025-02-03", "storage_temperature": -80.0, "cell_temperature": 20.0, "exposure_time": 0.1, "number_of_frames": 4, "wavelength": 0.1127, "sample_detector_distance": 1.7, "concentration_min": null, "concentration_max": 8.0, "sample_volume": 0.05, "flow_rate": 0.05, "s_min": 0.06, "s_max": 5.045, "total_exposure_time": null, "seccolumn": 1 }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDXX4_fit1_model1_img.png", "software": "AlphaFold", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDXX4_fit1_model1.pdb", "model_mw": 73.29, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 1234 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDXX4_fit1_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 4.912, "p_value": 0.0, "fit_residual_plot": "SASDXX4_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDXX4_fit1.fit", "fit_log": null, "software_version": null, "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "4.1", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of PgaB in phosphate-buffered saline, pH 7.4 were collected on the BL4-2 beam line at the Stanford Synchrotron Radiation Lightsource (SSRL; Menlo Park, CA, USA) using a Pilatus3 X 1M detector at a sample-detector distance of 1.7 m and at a wavelength of λ = 0.1127 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 0.05 μl sample at 8 mg/ml was injected at a 0.05 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 20°C. Four successive 0.100 second frames were collected. 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": 69.8, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 69.8, "porod_mw_error": null, "pddf_i0": 13.3, "pddf_i0_error": null, "guinier_i0": 13.2814, "guinier_i0_error": null, "pddf_rg": 2.87, "pddf_rg_error": null, "guinier_rg": 2.856, "guinier_rg_error": 0.007, "pddf_dmax": 9.43, "pddf_dmax_error": null, "porod_volume": 101.68, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 30, "guinier_point_last": 75, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDXX4_datloglog_img.png", "symmetry": null, "last_modified": "2025-11-24T10:26:41.769576+01:00", "bragg_peak": [] }