{ "code": "SASDW84", "status": "Published", "type_of_curve": "Co-flow batch", "angular_unit": "1/nm", "project": { "title": "The CRISPR-Cas9 knockout DDC SH-SY5Y in vitro model for AADC deficiency provides insight into the pathogenicity of R347Q and L353P variants: a cross-sectional structural and functional analysis.", "publication": { "title": "The CRISPR-Cas9 knockout DDC SH-SY5Y in vitro model for AADC deficiency provides insight into the pathogenicity of R347Q and L353P variants: a cross-sectional structural and functional analysis.", "author_list": "Carmona-Carmona CA, Bisello G, Franchini R, Lunardi G, Galavotti R, Perduca M, Ribeiro RP, Belviso BD, Giorgetti A, Caliandro R, Lievens PM, Bertoldi M", "journal": "FEBS J", "doi": "10.1111/febs.70120", "pmid": "40318155", "published_date": "2025 May 3" }, "status": "released", "submitted_date": "2024-12-20", "released_date": "2025-04-02" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDW84.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDW84.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDW84_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDW84_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDW84_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDW84_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDW84.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus3 2M", "resolution": 0.172 }, "name": "ESRF", "city": "Grenoble", "country": "France", "beamline_name": "BM29", "beam_geometry": "point", "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": "Aromatic-L-amino-acid decarboxylase (R347Q)", "short_name": "AADC", "sequence": "MNASEFRRRGKEMVDYMANYMEGIEGRQVYPDVEPGYLRPLIPAAAPQEPDTFEDIINDV\r\nEKIIMPGVTHWHSPYFFAYFPTASSYPAMLADMLCGAIGCIGFSWAASPACTELETVMMD\r\nWLGKMLELPKAFLNEKAGEGGGVIQGSASEATLVALLAARTKVIHRLQAASPELTQAAIM\r\nEKLVAYSSDQAHSSVERAGLIGGVKLKAIPSDGNFAMRASALQEALERDKAAGLIPFFMV\r\nATLGTTTCCSFDNLLEVGPICNKEDIWLHVDAAYAGSAFICPEFRHLLNGVEFADSFNFN\r\nPHKWLLVNFDCSAMWVKKRTDLTGAFRLDPTYLKHSHQDSGLITDYQHWQIPLGRRFRSL\r\nKMWFVFRMYGVKGLQAYIRKHVQLSHEFESLVRQDPRFEICVEVILGLVCFRLKGSNKVN\r\nEALLQRINSAKKIHLVPCHLRDKFVLRFAICSRTVESAHVQRAWEHIKELAADVLRAERE", "organism": "Homo sapiens", "uniprot_code": "P20711", "uniprot_range_first": 1, "uniprot_range_last": 478, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MNASEFRRRGKEMVDYMANYMEGIEGRQVYPDVEPGYLRPLIPAAAPQEPDTFEDIINDV\nEKIIMPGVTHWHSPYFFAYFPTASSYPAMLADMLCGAIGCIGFSWAASPACTELETVMMD\nWLGKMLELPKAFLNEKAGEGGGVIQGSASEATLVALLAARTKVIHRLQAASPELTQAAIM\nEKLVAYSSDQAHSSVERAGLIGGVKLKAIPSDGNFAMRASALQEALERDKAAGLIPFFMV\nATLGTTTCCSFDNLLEVGPICNKEDIWLHVDAAYAGSAFICPEFRHLLNGVEFADSFNFN\nPHKWLLVNFDCSAMWVKKRTDLTGAFRLDPTYLKHSHQDSGLITDYRHWQIPLGRRFRSL\nKMWFVFRMYGVKGLQAYIRKHVQLSHEFESLVRQDPRFEICVEVILGLVCFRLKGSNKVN\nEALLQRINSAKKIHLVPCHLRDKFVLRFAICSRTVESAHVQRAWEHIKELAADVLRAERE", "mw": 53.898, "total_mw": 107.796, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "" } ], "buffer": { "name": "50 mM HEPES, 100 µM pyridoxal 5'-phosphate", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.4, "deuteration": null }, "purity_method": null, "name": "Aromatic-L-amino-acid decarboxylase R347Q bound to pyridoxal 5'-phosphate (PLP)", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": null, "full_name": "National Research Council", "webpage": null } ], "contributor_name": "Benny Danilo", "contributor_surname": "Belviso", "orcid": "https://orcid.org/0000-0003-2880-1064" } ], "concentration_method": null, "concentration_unit": null, "date": "2021-07-07", "storage_temperature": 4.0, "cell_temperature": 4.0, "exposure_time": 5.0, "number_of_frames": 4, "wavelength": 0.1, "sample_detector_distance": 2.867, "concentration_min": 5.37, "concentration_max": 5.37, "sample_volume": 50.0, "flow_rate": 0.16, "s_min": 0.041, "s_max": 5.174, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDW84_fit1_model1_img.png", "software": "DAMMIN", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "3.0.2", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDW84_fit1_model1.pdb", "model_mw": 107.27, "bead_radius": 3.5, "log": "https://www.sasbdb.org/media/log_files/dammin_P1_refinement_AFfcoi5.log", "symmetry": null, "comment": null, "user": 930 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDW84_fit1_fixed_fit_img.png", "software": "DAMMIN", "chi_square_value": 1.14, "p_value": 0.1689, "fit_residual_plot": "SASDW84_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDW84_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/dammin_P1_refinement_YfauvID.log", "software_version": "3.0.2", "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": "Pyridoxal 5'-phosphate: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:18405. CAUTION: Potentially aggregated.", "experiment_description": "Synchrotron SAXS data from solutions of aromatic-L-amino-acid decarboxylase (R347Q) bound to pyridoxal 5'-phosphate in 50 mM HEPES, 100 µM pyridoxal 5'-phosphate, pH 7.4 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus3 2M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 5.4 and 5.4 mg/ml were measured at 4°C. Four successive 5 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": 114.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 151.432, "porod_mw_error": null, "pddf_i0": 548.1, "pddf_i0_error": null, "guinier_i0": 564.768, "guinier_i0_error": null, "pddf_rg": 3.589, "pddf_rg_error": null, "guinier_rg": 3.6, "guinier_rg_error": 0.02, "pddf_dmax": 14.15, "pddf_dmax_error": null, "porod_volume": 219.98, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 37, "guinier_point_last": 54, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDW84_datloglog_img.png", "symmetry": null, "last_modified": "2025-05-08T08:55:24.409452+02:00", "bragg_peak": [] }