{ "code": "SASDWE4", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/nm", "project": { "title": "Structural plasticity of 2A proteins in the Parechovirus family", "publication": null, "status": "released", "submitted_date": "2025-01-06", "released_date": "2026-01-06" }, "pddf_data": null, "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDWE4.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWE4_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWE4_kratky_img.png", "pddf_plot": null, "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWE4_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDWE4.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 6M", "resolution": null }, "name": "PETRA III", "city": "DESY; Hamburg", "country": "Germany", "beamline_name": "EMBL P12", "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": "Genome polyprotein (Protein 2A H-NC; Δ130-150)", "short_name": "HPeV1-2A (1-129)", "sequence": "GPGSPYGQQPQNRMMKLAYLDRGFYKHYGIIVGDHVYQLDSDDIFKTALTGKAKFTKTKLTSDWVIEEECELDYFRIKYLESAVDSEHIFSVDKNCETIAKDIFGTHTLSQHQAIGLVGTILLTAGLMSTIK", "organism": "Human parechovirus 1 (strain Harris)", "uniprot_code": "Q66578", "uniprot_range_first": 774, "uniprot_range_last": 902, "oligomerization": "other", "molecular_type": "protein", "uniprot_sequence": "METIKSIADMATGVVSSVDSTINAVNEKVESVGNEIGGNLLTKVADDASNILGPNCFATT\nAEPENKNVVQATTTVNTTNLTQHPSAPTMPFSPDFSNVDNFHSMAYDITTGDKNPSKLVR\nLETHEWTPSWARGYQITHVELPKVFWDHQDKPAYGQSRYFAAVRCGFHFQVQVNVNQGTA\nGSALVVYEPKPVVTYDSKLEFGAFTNLPHVLMNLAETTQADLCIPYVADTNYVKTDSSDL\nGQLKVYVWTPLSIPTGSANQVDVTILGSLLQLDFQNPRVFAQDVNIYDNAPNGKKKNWKK\nIMTMSTKYKWTRTKIDIAEGPGSMNMANVLCTTGAQSVALVGERAFYDPRTAGSKSRFDD\nLVKIAQLFSVMADSTTPSENHGVDAKGYFKWSATTAPQSIVHRNIVYLRLFPNLNVFVNS\nYSYFRGSLVLRLSVYASTFNRGRLRMGFFPNATTDSTSTLDNAIYTICDIGSDNSFEITI\nPYSFSTWMRKTNGHPIGLFQIEVLNRLTYNSSSPSEVYCIVQGKMGQDARFFCPTGSVVT\nFQNSWGSQMDLTDPLCIEDDTENCKQTMSPNELGLTSAQDDGPLGQEKPNYFLNFRSMNV\nDIFTVSHTKVDNLFGRAWFFMEHTFTNEGQWRVPLEFPKQGHGSLSLLFAYFTGELNIHV\nLFLSERGFLRVAHTYDTSNDRVNFLSSNGVITVPAGEQMTLSAPYYSNKPLRTVRDNNSL\nGYLMCKPFLTGTSTGKIEVYLSLRCPNFFFPLPAPKVTSSRALRGDMANLTNQSPYGQQP\nQNRMMKLAYLDRGFYKHYGIIVGDHVYQLDSDDIFKTALTGKAKFTKTKLTSDWVIEEEC\nELDYFRIKYLESAVDSEHIFSVDKNCETIAKDIFGTHTLSQHQAIGLVGTILLTAGLMST\nIKTPVNAVTIKEFFNHAIDGDEQGLSLLVQKCTTFFSSAATEILDNDLVKFIVKILVRIL\nCYMVLYCHKPNILTTACLSTLLIMDVTSSSVLSPSCKALMQCLMDGDVKKLAEIVAESMS\nNTDDDEVKEQICDTVKYTKTILSNQGPFKGFNEVSTAFRHIDWWIHTLLKIKDMVLSVFK\nPSIESKAIQWLERNKEHVCSILDYASDIIVESKDQSKMKTQDFYQRYSDCLAKFKPIMAI\nCFRSCHNSISNTVYRLFQELARIPNRISTNNDLIRIEPIGIWIQGEPGQGKSFLTHTLSR\nQLQKSCKLNGVFTNPTASEFMDGYDNQDIHLIDDLGQTRKEKDIEMLCNCISSVPFIVPM\nAHLEEKGKFYTSKLVVATTNKSDFSSTVLQDSGALKRRFPYIMHIRAAKAYSKAGKLNVS\nQAMATMSTGECWEVSKNGRDWETLKLKDLVDKITIDYNERVKNYNAWKQQLENQTLDDLD\nDAVSYIKHNFPDAIPYVDEYLNIEMSTLIEQMEAFIEPKPSVFKCFANKIGSKISKASRE\nVVDWFSDKIKSMLSFVERNKAWLTVVSAVTSAISILLLVTKIFKKEESKDERAYNPTLPV\nAKPKGTFPVSQREFKNEAPYDGQLEHIISQMAYITGSTTGHMTHCAGYQHDEIILHGHSI\nKYLEQEDELTLHYKNKVFPIEQPSVTQVTLGGKPMDLAILKCKLPFRFKKNSKYYTNKIG\nTESMLIWMTEQGIITKEVQRVHHSGGIKTREGTESTKTISYTVKSCKGMCGGLLISKVEG\nNFKILGMHIAGNGEMGVAIPFNFLKNDMSDQGIVTEITPIQPMYINTKTQIHKSPVYGAV\nEVKMGPAVLSKSDTRLEEPVECLIKKSASKYRVNKFQVNNELWQGVKACVKSKFREIFGM\nNGIVDMKTAILGTSHVNSMDLSTSAGYSFVKSGYKKKDLICLEPFSVAPLLERLVQDKFH\nNLLKGNQITTTFNTCLKDELRKLDKIASGKTRCIEACEVDYCIVYRMIMMEIYDKIYQTP\nCYYSGLAVGINPYKDWHFMINALNDYNYEMDYSQYDGSLSSMLLWEAVEVLAYCHDSPDL\nVMQLHKPVIDSDHVVFNERWLIHGGMPSGSPCTTVLNSLCNLMMCIYTTNLISPGIDCLP\nIVYGDDVILSLDKEIEPEKLQSIMADSFGAEVTGSRKDEPPSLKPRMEVEFLKRKPGYFP\nESTFIVGKLDTENMIQHLMWMKNFSTFKQQLQSYLMELCLHGKDTYQHYIKILEPYLQEW\nNITVDDYDVVITKLMPMVFD", "mw": 14.868, "total_mw": 14.868, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "The C-terminal truncated (short form) of nonstructural 2A protein of the human parechovirus 1 (Protein 2A H-NC; Δ130-150). The protein consrtuct used for SAXS contains an addtional non-native three amino acids at the N-terminus (GPG)." } ], "buffer": { "name": "20 mM HEPES, 150 mM NaCl, 5 mM DDT", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.4, "deuteration": null }, "purity_method": null, "name": "The nonstructural 2A protein of the human parechovirus 1 (HPeV1) short form, amino acids 1-129", "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": "Linköping University ", "webpage": null } ], "contributor_name": "Zuzanna", "contributor_surname": "Pietras", "orcid": "" } ], "concentration_method": null, "concentration_unit": null, "date": "2018-05-28", "storage_temperature": 10.0, "cell_temperature": 10.0, "exposure_time": 0.05, "number_of_frames": 30, "wavelength": 0.124, "sample_detector_distance": 3.0, "concentration_min": null, "concentration_max": 2.84, "sample_volume": null, "flow_rate": null, "s_min": 0.026, "s_max": 7.264, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDWE4_fit1_model1_img.png", "software": "PDB (Protein Data Bank)", "pdb_link": [ { "pdb_code": "7zu4", "ext_code": "7ZU4", "ext_type": "pdb", "difference_with_model": "identical" } ], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDWE4_fit1_model1.pdb", "model_mw": 13.89, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 733 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDWE4_fit1_model2_img.png", "software": "PDB (Protein Data Bank)", "pdb_link": [ { "pdb_code": "7zu4", "ext_code": "7ZU4", "ext_type": "pdb", "difference_with_model": "identical" } ], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDWE4_fit1_model2.pdb", "model_mw": 27.26, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 733 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDWE4_fit1_model3_img.png", "software": "PDB (Protein Data Bank)", "pdb_link": [ { "pdb_code": "7zu4", "ext_code": "7ZU4", "ext_type": "pdb", "difference_with_model": "identical" } ], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDWE4_fit1_model3.pdb", "model_mw": 54.52, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 733 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDWE4_fit1_model4_img.png", "software": "PDB (Protein Data Bank)", "pdb_link": [ { "pdb_code": "7zu4", "ext_code": "7ZU4", "ext_type": "pdb", "difference_with_model": "identical" } ], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDWE4_fit1_model4.pdb", "model_mw": 81.78, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 733 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWE4_fit1_fixed_fit_img.png", "software": "OLIGOMER", "chi_square_value": 0.99, "p_value": 0.2912, "fit_residual_plot": "SASDWE4_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDWE4_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/oligomer_Faqn5Cz.log", "software_version": null, "description": "" } ], "estimated_volume_method": null, "pddf_software": null, "pddf_software_version": null, "i0_calibration_standard": null, "description": "The HPeV1-2A (1-129) sample was measured at various sample concentrations. For this entry the 2.84 mg/ml sample scattering is displayed, while measurements spanning seven dilutions are made available in the full entry zip archive. Mixture analysis of the scattering profiles was performed with the program OLIGOMER. The OLIGOMER results show that HPeV1-2A is a mixture of monomers (74%), dimers (10.6%), tetramers (13%), hexamers (0.24%), based on the volume-fraction weighted form factors calculated from the X-ray crystal structure, PDB ID: 7ZU4 (dimer) and derived monomer, tetramer and hexamer (based on crystal packing).", "experiment_description": "Synchrotron SAXS data from solutions of the nonstructural 2A protein of human parechovirus 1 (HPeV1-2A) in 20 mM HEPES, 150 mM NaCl, 5 mM DDT, pH 7.4 were collected on the EMBL P12 beam line at PETRA III (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 2.84 mg/ml was measured at 10°C. 30 successive 0.050 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": null, "experimental_mw": 18.675, "experimental_mw_error": null, "guinier_i0_mw": 18.044, "guinier_i0_mw_error": null, "porod_mw": 26.0, "porod_mw_error": null, "pddf_i0": null, "pddf_i0_error": null, "guinier_i0": 0.013517, "guinier_i0_error": null, "pddf_rg": null, "pddf_rg_error": null, "guinier_rg": 2.02, "guinier_rg_error": 0.012, "pddf_dmax": 9.5, "pddf_dmax_error": null, "porod_volume": 42.7, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 31, "guinier_point_last": 226, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDWE4_datloglog_img.png", "symmetry": null, "last_modified": "2026-01-14T11:33:40.183934+01:00", "bragg_peak": [] }