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{
"code": "SASDW47",
"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/SASDW47.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDW47.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDW47_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDW47_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDW47_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDW47_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDW47.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-RFP-St",
"short_name": "DRSt",
"sequence": ">DRSt\r\nMAKSGNYSYKRWVFTINNPTFEDYVHVLEFCTLDNCKFAIVGEEKGANGTPHLQGFLNLRSNARAAALEESLGGRAWLSRARGSDEDNEEYCAKESTYLRVGEPVSKGRSSGSGASSEDVIKEFMRFKVRMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQFQYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASTERMYPEDGALKGEIKMRLKLKDGGHYDAEVKTTYMAKKPVQLPGAYKTDIKLDITSHNEDYTIVEQYERRHSTGAGSGAHIVMVDAYKPTKGSGWSHPQFEK",
"organism": "synthetic construct",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "",
"mw": 40.501,
"total_mw": 40.501,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "A chimeric protein consisting of DCV, RFP, and SpyTag domain. DCV is an endonuclease ssDNA binding domain originated from Muscovy duck circovirus, RFP is a red fluorescent protein."
},
{
"long_name": "DCV-RFP-St",
"short_name": "DRSt",
"sequence": ">DRSt\r\nMAKSGNYSYKRWVFTINNPTFEDYVHVLEFCTLDNCKFAIVGEEKGANGTPHLQGFLNLRSNARAAALEESLGGRAWLSRARGSDEDNEEYCAKESTYLRVGEPVSKGRSSGSGASSEDVIKEFMRFKVRMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQFQYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASTERMYPEDGALKGEIKMRLKLKDGGHYDAEVKTTYMAKKPVQLPGAYKTDIKLDITSHNEDYTIVEQYERRHSTGAGSGAHIVMVDAYKPTKGSGWSHPQFEK",
"organism": "synthetic construct",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "",
"mw": 40.501,
"total_mw": 40.501,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "A chimeric protein consisting of DCV, RFP, and SpyTag domain. DCV is an endonuclease ssDNA binding domain originated from Muscovy duck circovirus, RFP is a red 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-2xDRSt - Coiled-Coil Tetrahedron with Four Functional Domains (2x SpyCatcher, RFP, DCV) and Dual SpyCatcher-SpyTag Linkages with DCV-RFP-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": "2024-09-24",
"storage_temperature": 10.0,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 3000,
"wavelength": 0.123985,
"sample_detector_distance": 3.0,
"concentration_min": null,
"concentration_max": 10.0,
"sample_volume": 80.0,
"flow_rate": 0.5,
"s_min": 0.087,
"s_max": 2.541,
"total_exposure_time": null,
"seccolumn": 47
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDW47_fit1_model1_img.png",
"software": "SREFLEX",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "3.2.1",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDW47_fit1_model1.pdb",
"model_mw": 190.0,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "The model was first generated by MODELLER (10.5) and later refined with SREFLEX.",
"user": 1027
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDW47_fit1_fixed_fit_img.png",
"software": "SREFLEX",
"chi_square_value": 2.7995,
"p_value": 0.0,
"fit_residual_plot": "SASDW47_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDW47_fit1.fit",
"fit_log": null,
"software_version": "3.2.1",
"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": "1/cm",
"experimental_mw": 196.8,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 305.0,
"porod_mw_error": null,
"pddf_i0": 29430.0,
"pddf_i0_error": null,
"guinier_i0": 29317.6,
"guinier_i0_error": null,
"pddf_rg": 5.174,
"pddf_rg_error": null,
"guinier_rg": 5.14,
"guinier_rg_error": 0.005,
"pddf_dmax": 15.4,
"pddf_dmax_error": 0.2,
"porod_volume": 480.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 60,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDW47_datloglog_img.png",
"symmetry": null,
"last_modified": "2025-08-01T07:48:35.911887+02:00",
"bragg_peak": []
}
