{ "code": "SASDW57", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/nm", "project": { "title": "Programmable Protein-DNA Composite Nanostructures: from Nanostructure Construction to Protein-Induced Micro-Scale Material Self-Assembly and Functionalization.", "publication": { "title": "Programmable Protein-DNA Composite Nanostructures: from Nanostructure Construction to Protein-Induced Micro-Scale Material Self-Assembly and Functionalization.", "author_list": "Zhou W, Strmšek Ž, Snoj J, Škarabot M, Jerala R", "journal": "Small", "doi": "10.1002/smll.202502060", "pmid": "40442952", "published_date": "2025 Jul" }, "status": "released", "submitted_date": "2025-02-06", "released_date": "2025-08-01" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDW57.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDW57.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDW57_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDW57_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDW57_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDW57_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDW57.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": "TET12-2Sc-RFP-DCV", "short_name": "SSRD", "sequence": ">SSRD\r\nMLEEELKQLEEELQAIEEQLAQLQWKAQARKEKLAQLKEKLSGPGSPEDEIQQLEEEISQLEQKNSELKEKNQELKYGSGPGDIEQELERAKESIRRLEQEVNQERSRMQYLQTLLEKSGPGQLEDKVEELLSKNYHLENEVERLKKLVGSGDSATHIKFSKRDEDGKELAGATMELRDSSGKTISTWISDGQVKDFYLYPGKYTFVETAAPDGYEVATAITFTVNEQGQVTVNGSGLEEELKQLEEELQAIEEQLAQLQWKAQARKEKLAQLKEKLSGPGSPEDEIQQLEEKNSQLKQEISQLEEKNQELKYGSGPGQLEDKVEELLSKNYHLENEVERLKKLVGSGPGSPEDKISQLKEKIQQLKQENQQLEEENSQLEYGSGDSATHIKFSKRDEDGKELAGATMELRDSSGKTISTWISDGQVKDFYLYPGKYTFVETAAPDGYEVATAITFTVNEQGQVTVNGSGSPEDENSQLEEKISQLKQKNSELKEEIQQLEYGSGPGSPEDKISELKEENQQLEQKIQQLKEENSQLEYGSGMASSEDVIKEFMRFKVRMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQFQYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASTERMYPEDGALKGEIKMRLKLKDGGHYDAEVKTTYMAKKPVQLPGAYKTDIKLDITSHNEDYTIVEQYERRHSTGAGSGDIEQELERAKESIRRLEQEVNQERSRMQYLQTLLEKSGPGSPEDKNSELKEEIQQLEEENQQLEEKISELKYGGSGKSGNYSYKRWVFTINNPTFEDYVHVLEFCTLDNCKFAIVGEEKGANGTPHLQGFLNLRSNARAAALEESLGGRAWLSRARGSDEDNEEYCAKESTYLRVGEPVSKGRSSLEHHHHHHHH", "organism": "synthetic construct", "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "", "mw": 109.029, "total_mw": 109.029, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "CCPO is short for coiled coil protein origami (CCPO) tetrahedron with 2 SpyCatcher domains, 1 RFP and 1 DCV domain inserted at each of 4 vertices. DCV is an endonuclease ssDNA binding domain originated from Muscovy duck circovirus and RFP is a red fluorescent protein." }, { "long_name": "DCV-GFP-St", "short_name": "DGSt", "sequence": ">DGSt\r\nMAKSGNYSYKRWVFTINNPTFEDYVHVLEFCTLDNCKFAIVGEEKGANGTPHLQGFLNLRSNARAAALEESLGGRAWLSRARGSDEDNEEYCAKESTYLRVGEPVSKGRSSSGKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATIGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGKYKTRAVVKFEGDTLVNRIELKGTDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKANFTVRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQTVLSKDPNEKRDHMVLHEYVNAAGITGSGGSGAHIVMVDAYKPTKGSGHHHHHHHH", "organism": "synthetic construct", "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "", "mw": 41.266, "total_mw": 41.266, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "A chimeric protein consisting of DCV, GFP, and SpyTag domain. DCV is an endonuclease ssDNA binding domain originated from Muscovy duck circovirus. GFP is a green fluorescent protein." }, { "long_name": "DCV-GFP-St", "short_name": "DGSt", "sequence": ">DGSt\r\nMAKSGNYSYKRWVFTINNPTFEDYVHVLEFCTLDNCKFAIVGEEKGANGTPHLQGFLNLRSNARAAALEESLGGRAWLSRARGSDEDNEEYCAKESTYLRVGEPVSKGRSSSGKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATIGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGKYKTRAVVKFEGDTLVNRIELKGTDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKANFTVRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQTVLSKDPNEKRDHMVLHEYVNAAGITGSGGSGAHIVMVDAYKPTKGSGHHHHHHHH", "organism": "synthetic construct", "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "", "mw": 41.266, "total_mw": 41.266, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "A chimeric protein consisting of DCV, GFP, and SpyTag domain. DCV is an endonuclease ssDNA binding domain originated from Muscovy duck circovirus. GFP is a green fluorescent protein." } ], "buffer": { "name": "20 mM Tris, 150 mM NaCL, 3% glycerol", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "SSRD-2xDGSt - Coiled-Coil Tetrahedron with Four Functional Domains (2x SpyCatcher, RFP, DCV) and Dual SpyCatcher-SpyTag Linkages with DCV-GFP-St Extension", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "KI", "address": "Ljubljana, Slovenia", "full_name": "Kemijski inštitut", "webpage": null } ], "contributor_name": "Jaka", "contributor_surname": "Snoj", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2024-03-18", "storage_temperature": 5.0, "cell_temperature": 20.0, "exposure_time": 1.0, "number_of_frames": 3000, "wavelength": 0.123982, "sample_detector_distance": 3.0, "concentration_min": null, "concentration_max": 8.0, "sample_volume": 40.0, "flow_rate": 0.7, "s_min": 0.069, "s_max": 2.501, "total_exposure_time": null, "seccolumn": 47 }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDW57_fit1_model1_img.png", "software": "MODELLER", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "10.5", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDW57_fit1_model1.pdb", "model_mw": 191.5, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 1027 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDW57_fit1_fixed_fit_img.png", "software": "Pepsi-SAXS", "chi_square_value": 3.6885, "p_value": 0.0, "fit_residual_plot": "SASDW57_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDW57_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Tet12SN_SSRD2xDCV_GFP_St_random_very_slow-397-1.log", "software_version": "3.0", "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": "Note: The experimentally determined protein mass (SEC-MALS) is overestimated due to the presence of a fluorescent protein in the sample. The light scattering laser operates at a wavelength that excites the fluorescent protein, leading to inaccurate signal measurements.", "experiment_description": null, "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 219.7, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 353.0, "porod_mw_error": null, "pddf_i0": 50610.0, "pddf_i0_error": null, "guinier_i0": 51629.6, "guinier_i0_error": null, "pddf_rg": 5.656, "pddf_rg_error": null, "guinier_rg": 5.79, "guinier_rg_error": 0.015, "pddf_dmax": 17.3, "pddf_dmax_error": 0.2, "porod_volume": 580.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 2, "guinier_point_last": 52, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDW57_datloglog_img.png", "symmetry": null, "last_modified": "2025-08-01T07:48:36.287518+02:00", "bragg_peak": [] }