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{
"code": "SASDEZ2",
"status": "Published",
"type_of_curve": "Extrapolated to infinite dilution",
"angular_unit": "1/nm",
"project": {
"title": "Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements.",
"publication": {
"title": "Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements.",
"author_list": "Fuertes G, Banterle N, Ruff KM, Chowdhury A, Mercadante D, Koehler C, Kachala M, Estrada Girona G, Milles S, Mishra A, Onck PR, Gräter F, Esteban-Martín S, Pappu RV, Svergun DI, Lemke EA",
"journal": "Proc Natl Acad Sci U S A",
"doi": "10.1073/pnas.1704692114",
"pmid": "28716919",
"published_date": "2017 Aug 1"
},
"status": "released",
"submitted_date": "2018-08-16",
"released_date": "2018-08-18"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEZ2.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEZ2.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEZ2_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEZ2_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEZ2_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEZ2_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEZ2.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 2M",
"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": "Nuclear pore complex protein Nup153",
"short_name": "NUL",
"sequence": "> U=p-acetylphenylalanine. \r\nGCGFKGFDTSSSSSNSAASSSFKFGVSSSSSGPSQTLTSTGNFKFGDQGGFKIGVSSDSGSINPMSEGFKFSKPIGDFKFGVSSESKPEEVKKDSKNDNFKFGLSSGLSNPVUA",
"organism": "Homo sapiens",
"uniprot_code": "P49790",
"uniprot_range_first": 884,
"uniprot_range_last": 993,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MASGAGGVGGGGGGKIRTRRCHQGPIKPYQQGRQQHQGILSRVTESVKNIVPGWLQRYFN\nKNEDVCSCSTDTSEVPRWPENKEDHLVYADEESSNITDGRITPEPAVSNTEEPSTTSTAS\nNYPDVLTRPSLHRSHLNFSMLESPALHCQPSTSSAFPIGSSGFSLVKEIKDSTSQHDDDN\nISTTSGFSSRASDKDITVSKNTSLPPLWSPEAERSHSLSQHTATSSKKPAFNLSAFGTLS\nPSLGNSSILKTSQLGDSPFYPGKTTYGGAAAAVRQSKLRNTPYQAPVRRQMKAKQLSAQS\nYGVTSSTARRILQSLEKMSSPLADAKRIPSIVSSPLNSPLDRSGIDITDFQAKREKVDSQ\nYPPVQRLMTPKPVSIATNRSVYFKPSLTPSGEFRKTNQRIDNKCSTGYEKNMTPGQNREQ\nRESGFSYPNFSLPAANGLSSGVGGGGGKMRRERTRFVASKPLEEEEMEVPVLPKISLPIT\nSSSLPTFNFSSPEITTSSPSPINSSQALTNKVQMTSPSSTGSPMFKFSSPIVKSTEANVL\nPPSSIGFTFSVPVAKTAELSGSSSTLEPIISSSAHHVTTVNSTNCKKTPPEDCEGPFRPA\nEILKEGSVLDILKSPGFASPKIDSVAAQPTATSPVVYTRPAISSFSSSGIGFGESLKAGS\nSWQCDTCLLQNKVTDNKCIACQAAKLSPRDTAKQTGIETPNKSGKTTLSASGTGFGDKFK\nPVIGTWDCDTCLVQNKPEAIKCVACETPKPGTCVKRALTLTVVSESAETMTASSSSCTVT\nTGTLGFGDKFKRPIGSWECSVCCVSNNAEDNKCVSCMSEKPGSSVPASSSSTVPVSLPSG\nGSLGLEKFKKPEGSWDCELCLVQNKADSTKCLACESAKPGTKSGFKGFDTSSSSSNSAAS\nSSFKFGVSSSSSGPSQTLTSTGNFKFGDQGGFKIGVSSDSGSINPMSEGFKFSKPIGDFK\nFGVSSESKPEEVKKDSKNDNFKFGLSSGLSNPVSLTPFQFGVSNLGQEEKKEELPKSSSA\nGFSFGTGVINSTPAPANTIVTSENKSSFNLGTIETKSASVAPFTCKTSEAKKEEMPATKG\nGFSFGNVEPASLPSASVFVLGRTEEKQQEPVTSTSLVFGKKADNEEPKCQPVFSFGNSEQ\nTKDENSSKSTFSFSMTKPSEKESEQPAKATFAFGAQTSTTADQGAAKPVFSFLNNSSSSS\nSTPATSAGGGIFGSSTSSSNPPVATFVFGQSSNPVSSSAFGNTAESSTSQSLLFSQDSKL\nATTSSTGTAVTPFVFGPGASSNNTTTSGFGFGATTTSSSAGSSFVFGTGPSAPSASPAFG\nANQTPTFGQSQGASQPNPPGFGSISSSTALFPTGSQPAPPTFGTVSSSSQPPVFGQQPSQ\nSAFGSGTTPNSSSAFQFGSSTTNFNFTNNSPSGVFTFGANSSTPAASAQPSGSGGFPFNQ\nSPAAFTVGSNGKNVFSSSGTSFSGRKIKTAVRRRK",
"mw": 11.717,
"total_mw": 11.717,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "PBS, 10 mM DTT",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.4,
"deuteration": null
},
"purity_method": null,
"name": "Unlabeled nuclear pore complex protein Nup153 (NUL) without denaturant",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Prague, Czech Republic",
"full_name": "Institute of Biotechnology CAS v.v.i.",
"webpage": "http://www.ibt.cas.cz/"
}
],
"contributor_name": "Gustavo",
"contributor_surname": "Fuertes Vives",
"orcid": "https://orcid.org/0000-0002-8564-8644"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2013-11-08",
"storage_temperature": null,
"cell_temperature": 23.0,
"exposure_time": 0.05,
"number_of_frames": 20,
"wavelength": 0.1,
"sample_detector_distance": 3.0,
"concentration_min": 2.0,
"concentration_max": 5.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.028,
"s_max": 4.45,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEZ2_fit1_model1_img.png",
"software": "Other",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEZ2_fit1_model1.pdb",
"model_mw": 11.73,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "p-acetylphenylalanine was replaced with a cysteine.",
"user": 359
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEZ2_fit1_model2_img.png",
"software": "Other",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEZ2_fit1_model2.pdb",
"model_mw": 11.73,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "p-acetylphenylalanine was replaced with a cysteine.",
"user": 359
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEZ2_fit1_model3_img.png",
"software": "Other",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "CAMPARI",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEZ2_fit1_model3.pdb",
"model_mw": 11.73,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "p-acetylphenylalanine was replaced with a cysteine.",
"user": 359
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEZ2_fit1_model4_img.png",
"software": "Other",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEZ2_fit1_model4.pdb",
"model_mw": 11.73,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "p-acetylphenylalanine was replaced with a cysteine.",
"user": 359
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEZ2_fit1_fixed_fit_img.png",
"software": "EOM/GAJOE",
"chi_square_value": 1.927,
"p_value": 1.2e-05,
"fit_residual_plot": "SASDEZ2_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEZ2_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/logFile_001_1_V45OAvk.log",
"software_version": null,
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "The protein contains a penultimate non-canonical amino acid p-acetylphenylalanine (207 Da) that is represented as U (selenocysteine, 168 Da) in the amino acid sequence for the entry. Therefore, the calculated MW from sequence (MW(expected)) must be adjusted accordingly (ca. 40 Da).",
"experiment_description": null,
"tags": [
"idp"
],
"intensity_unit": "arbitrary",
"experimental_mw": 23.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 660.1,
"pddf_i0_error": 2.6,
"guinier_i0": 654.3,
"guinier_i0_error": 4.5,
"pddf_rg": 3.174,
"pddf_rg_error": 0.02,
"guinier_rg": 3.0,
"guinier_rg_error": 0.31,
"pddf_dmax": 10.93,
"pddf_dmax_error": null,
"porod_volume": 31.68,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 10,
"guinier_point_last": 153,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDEZ2_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}
