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{
"code": "SASDD65",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "Insights into catalysis and function of phosphoribosyl-linked serine ubiquitination.",
"publication": {
"title": "Insights into catalysis and function of phosphoribosyl-linked serine ubiquitination.",
"author_list": "Kalayil S, Bhogaraju S, Bonn F, Shin D, Liu Y, Gan N, Basquin J, Grumati P, Luo ZQ, Dikic I",
"journal": "Nature",
"doi": "10.1038/s41586-018-0145-8",
"pmid": "29795347",
"published_date": "2018 May"
},
"status": "released",
"submitted_date": "2018-03-19",
"released_date": "2018-05-29"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDD65.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDD65.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD65_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD65_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDD65_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD65_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDD65.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": "Ubiquitinating/deubiquitinating enzyme SdeA",
"short_name": "SdeA",
"sequence": "HGLSHTLRTMAYAELIV\r\nEEARKAKLRGETLGKFKDGRTIADVTPQELKKIMIAQAFFVAGRDDEASDAKNYQKYHEQ\r\nSRDAFLKYVKDNESTLIPDVFKDQEDVNFYARVIEDKSHDWESTPAHVLINQGHMVDLVR\r\nVKQPPESFLQRYFSSMQRWIGSQATEAVFGIQRQFFHATYEVVAGFDSDNKEPHLVVSGL\r\nGRYVIGEDGQPIREAPKKGQKEGDLKVFPQTYKLKENERLMRVDEFLKLPEIQNTFPGSG\r\nKHLQGGMPGMNEMDYWNRLNSLNRARCENDVDFCLKQLQTAHDKAKIEPIKQAFQSSKGK\r\nERRQPNVDEIAAARIIQQILANPDCIHDDHVLINGQKLEQQFFRDLLAKCEMAVVGSLLN\r\nDTDIGNIDTLMRHEKDTEFHSTNPEAVPVKIGEYWINDQRINNSSGNITQKKHDLIFLMQ\r\nNDAWYFSRVNAIAQNRDKGSTFKEVLITTLMTPLTSKALVDTSQAKPPTRLFRGLNLSEE\r\nFTKGLIDQANAMIANTTERLFTDHSPEAFKQIKLNDLSKMSGRTNASTTTEIKLVKETWD\r\nSNVIFEMLDPDGLLHSKQVGRHGEGTESEFSVYLPEDVALVPVKVTLDGKTQKGENRYVF\r\nTFVAVKSPDFTPRH",
"organism": "Legionella pneumophila subsp. pneumophila",
"uniprot_code": "Q5ZTK4",
"uniprot_range_first": 277,
"uniprot_range_last": 907,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MPKYVEGVELTQEGMHAIFARMGYGDITSGSIYNGVPTIDTGALNRQGFMPVLTGVGPHR\nDSGHWIMLIKGPGNQYYLFDPLGKTSGEGYQNILAAQLPMGSTLSVIPNGSGLNMGLCGY\nWVASAGLRAHQALNQHNPPTLLNVGQTITNEMRNELDHDGYRKITGWLRAVADEFPEGDP\nQLDGKALRENTEKDLKIEIPTLVLPGKDTSPKEMSVKPTAPQDKSVPVWNGFSLYTDDTV\nKAAAQYAYDNYLGKPYTGSVESAPANFGGRMVYRQHHGLSHTLRTMAYAELIVEEARKAK\nLRGETLGKFKDGRTIADVTPQELKKIMIAQAFFVAGRDDEASDAKNYQKYHEQSRDAFLK\nYVKDNESTLIPDVFKDQEDVNFYARVIEDKSHDWESTPAHVLINQGHMVDLVRVKQPPES\nFLQRYFSSMQRWIGSQATEAVFGIQRQFFHATYEVVAGFDSDNKEPHLVVSGLGRYVIGE\nDGQPIREAPKKGQKEGDLKVFPQTYKLKENERLMRVDEFLKLPEIQNTFPGSGKHLQGGM\nPGMNEMDYWNRLNSLNRARCENDVDFCLKQLQTAHDKAKIEPIKQAFQSSKGKERRQPNV\nDEIAAARIIQQILANPDCIHDDHVLINGQKLEQQFFRDLLAKCEMAVVGSLLNDTDIGNI\nDTLMRHEKDTEFHSTNPEAVPVKIGEYWINDQRINNSSGNITQKKHDLIFLMQNDAWYFS\nRVNAIAQNRDKGSTFKEVLITTLMTPLTSKALVDTSQAKPPTRLFRGLNLSEEFTKGLID\nQANAMIANTTERLFTDHSPEAFKQIKLNDLSKMSGRTNASTTTEIKLVKETWDSNVIFEM\nLDPDGLLHSKQVGRHGEGTESEFSVYLPEDVALVPVKVTLDGKTQKGENRYVFTFVAVKS\nPDFTPRHESGYAVEPFLRMQAAKLAEVKSSIEKAQRAPDLETIFNLQNEVEAVQYSHLST\nGYKNFLKNTVGPVLENSLSGLMESDTDTLSKALAAFPSDTQWSAFNFEEARQAKRQMDAI\nKQMVGNKVVLDALTQCQDALEKQNIAGALDALKKIPSEKEMGTIRRELREQIQSARQELE\nSLQRAVVTPVVTDEKKVRERYDALIENTSKKITELETGKLPNLDAVKKGISNLSNLKQEV\nTVLRNEKIRMHVGTDKVDFSDVEKLEQQIQVIDTKLADAYLLEVTKQISALDNTKPKNQT\nELKTKIAAFLDRTTDIEMLRNERIKKHGSSKDPLDLSDLDKLSGSLQRINQSLVSDLITT\nIRVSINQMEAKTFHEQEKEIQQNFELLAKLEKTLDKSKTSEKLREDIPKLNDLLVAKQKA\nYPQMVQMQLKSEVFVTQLREVCQANHDDLDKTRNARLRELDRLDREAGITRMVGNLIWGL\nTNKVGLTTDERLDIRTKQQSLARFKNELFNDKIDTDQLISNLARKRPSELQEGLGISTDN\nAMELHLLLTELAGKTTSPDELEERMKAIDDISTKIGREPEHLKFVMVEEDESNKKTIGF",
"mw": 71.811,
"total_mw": 71.811,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "10 mM HEPES 150 mM NaCl 1 mM TCEP",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Ubiquitinating/deubiquitinating enzyme SdeA 207 914",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "IBCII",
"address": "Germany",
"full_name": "IBCII, Goethe University-Medical Faculty",
"webpage": "https://www.biochem2.com/"
}
],
"contributor_name": "Donghyuk",
"contributor_surname": "Shin",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-11-26",
"storage_temperature": 10.0,
"cell_temperature": 10.0,
"exposure_time": 0.045,
"number_of_frames": 20,
"wavelength": 0.124,
"sample_detector_distance": 3.0,
"concentration_min": null,
"concentration_max": 2.64,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.061,
"s_max": 3.893,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD65_fit1_model1_img.png",
"software": "DAMMIN",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDD65_fit1_model1.pdb",
"model_mw": 80.155,
"bead_radius": 3.25,
"log": "https://www.sasbdb.org/media/log_files/wo_crop.log",
"symmetry": null,
"comment": null,
"user": 298
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD65_fit1_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 1.053,
"p_value": 0.547735,
"fit_residual_plot": "SASDD65_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDD65_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/wo_crop_zyam680.log",
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD65_fit2_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/SASDD65_fit2_model1.pdb",
"model_mw": 69.9,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 298
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD65_fit2_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.84,
"p_value": 0.0,
"fit_residual_plot": "SASDD65_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDD65_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/SdeA_open200.log",
"software_version": null,
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of Ubiquitinating/deubiquitinating enzyme, SdeA, in 10 mM HEPES 150 mM NaCl 1 mM TCEP, pH 7.5, were collected on the EMBL-P12 bioSAXS beam line at PETRA III (DESY, Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 2.64 mg/ml was measured at 10°C. 20 successive 0.045 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": "1/cm",
"experimental_mw": 73.0,
"experimental_mw_error": null,
"guinier_i0_mw": 80.0,
"guinier_i0_mw_error": null,
"porod_mw": 80.0,
"porod_mw_error": null,
"pddf_i0": 0.05686,
"pddf_i0_error": 7.55e-05,
"guinier_i0": 0.057,
"guinier_i0_error": 7.3e-05,
"pddf_rg": 3.475,
"pddf_rg_error": 0.006,
"guinier_rg": 3.45,
"guinier_rg_error": 0.03,
"pddf_dmax": 11.2,
"pddf_dmax_error": null,
"porod_volume": 128.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 5,
"guinier_point_last": 111,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDD65_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}
