查看完整 summary.json 原文
{
"code": "SASDEL9",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Complementary substrate specificity and distinct quaternary assembly of the <i>Escherichia coli</i> aerobic and anaerobic beta-oxidation trifunctional enzyme complexes.",
"publication": {
"title": "Complementary substrate specificity and distinct quaternary assembly of the <i>Escherichia coli</i> aerobic and anaerobic beta-oxidation trifunctional enzyme complexes.",
"author_list": "Sah-Teli SK, Hynönen MJ, Schmitz W, Geraets JA, Seitsonen J, Pedersen JS, Butcher SJ, Wierenga RK, Venkatesan R",
"journal": "Biochem J",
"doi": "10.1042/BCJ20190314",
"pmid": "31235482",
"published_date": "2019 Jun 25"
},
"status": "released",
"submitted_date": "2018-12-28",
"released_date": "2019-07-02"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEL9.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEL9.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEL9_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEL9_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEL9_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEL9_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEL9.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 2M",
"resolution": null
},
"name": "Diamond Light Source",
"city": "Didcot",
"country": "UK",
"beamline_name": "B21",
"beam_geometry": "1 x 5 mm",
"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": "Fatty acid oxidation complex subunit alpha",
"short_name": "EcTFE-alpha",
"sequence": ">EcTFE-alpha\r\nMGSSHHHHHHSQDPMLYKGDTLYLDWLEDGIAELVFDAPGSVNKLDTATVASLGEAIGVLEQQSDLKGLLLRSNKAAFIVGADITEFLS\r\nLFLVPEEQLSQWLHFANSVFNRLEDLPVPTIAAVNGYALGGGCECVLATDYRLATPDLRIGLPETKLGIMPGFGG\r\nSVRMPRMLGADSALEIIAAGKDVGADQALKIGLVDGVVKAEKLVEGAKAVLRQAINGDLDWKAKRQPKLEPLKLS\r\nKIEATMSFTIAKGMVAQTAGKHYPAPITAVKTIEAAARFGREEALNLENKSFVPLAHTNEARALVGIFLNDQYVK\r\nGKAKKLTKDVETPKQAAVLGAGIMGGGIAYQSAWKGVPVVMKDINDKSLTLGMTEAAKLLNKQLERGKIDGLKLA\r\nGVISTIHPTLDYAGFDRVDIVVEAVVENPKVKKAVLAETEQKVRQDTVLASNTSTIPISELANALERPENFCGMH\r\nFFNPVHRMPLVEIIRGEKSSDETIAKVVAWASKMGKTPIVVNDCPGFFVNRVLFPYFAGFSQLLRDGADFRKIDK\r\nVMEKQFGWPMGPAYLLDVVGIDTAHHAQAVMAAGFPQRMQKDYRDAIDALFDANRFGQKNGLGFWRYKEDSKGKP\r\nKKEEDAAVEDLLAEVSQPKRDFSEEEIIARMMIPMVNEVVRCLEEGIIATPAEADMALVYGLGFPPFHGGAFRWL\r\nDTLGSAKYLDMAQQYQHLGPLYEVPEGLRNKARHNEPYYPPVEPARPVGDLKTA",
"organism": "Escherichia coli",
"uniprot_code": "P21177",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MLYKGDTLYLDWLEDGIAELVFDAPGSVNKLDTATVASLGEAIGVLEQQSDLKGLLLRSN\nKAAFIVGADITEFLSLFLVPEEQLSQWLHFANSVFNRLEDLPVPTIAAVNGYALGGGCEC\nVLATDYRLATPDLRIGLPETKLGIMPGFGGSVRMPRMLGADSALEIIAAGKDVGADQALK\nIGLVDGVVKAEKLVEGAKAVLRQAINGDLDWKAKRQPKLEPLKLSKIEATMSFTIAKGMV\nAQTAGKHYPAPITAVKTIEAAARFGREEALNLENKSFVPLAHTNEARALVGIFLNDQYVK\nGKAKKLTKDVETPKQAAVLGAGIMGGGIAYQSAWKGVPVVMKDINDKSLTLGMTEAAKLL\nNKQLERGKIDGLKLAGVISTIHPTLDYAGFDRVDIVVEAVVENPKVKKAVLAETEQKVRQ\nDTVLASNTSTIPISELANALERPENFCGMHFFNPVHRMPLVEIIRGEKSSDETIAKVVAW\nASKMGKTPIVVNDCPGFFVNRVLFPYFAGFSQLLRDGADFRKIDKVMEKQFGWPMGPAYL\nLDVVGIDTAHHAQAVMAAGFPQRMQKDYRDAIDALFDANRFGQKNGLGFWRYKEDSKGKP\nKKEEDAAVEDLLAEVSQPKRDFSEEEIIARMMIPMVNEVVRCLEEGIIATPAEADMALVY\nGLGFPPFHGGAFRWLDTLGSAKYLDMAQQYQHLGPLYEVPEGLRNKARHNEPYYPPVEPA\nRPVGDLKTA",
"mw": 81.206,
"total_mw": 81.206,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Fatty acid oxidation complex subunit alpha",
"short_name": "EcTFE-alpha",
"sequence": ">EcTFE-alpha\r\nMGSSHHHHHHSQDPMLYKGDTLYLDWLEDGIAELVFDAPGSVNKLDTATVASLGEAIGVLEQQSDLKGLLLRSNKAAFIVGADITEFLS\r\nLFLVPEEQLSQWLHFANSVFNRLEDLPVPTIAAVNGYALGGGCECVLATDYRLATPDLRIGLPETKLGIMPGFGG\r\nSVRMPRMLGADSALEIIAAGKDVGADQALKIGLVDGVVKAEKLVEGAKAVLRQAINGDLDWKAKRQPKLEPLKLS\r\nKIEATMSFTIAKGMVAQTAGKHYPAPITAVKTIEAAARFGREEALNLENKSFVPLAHTNEARALVGIFLNDQYVK\r\nGKAKKLTKDVETPKQAAVLGAGIMGGGIAYQSAWKGVPVVMKDINDKSLTLGMTEAAKLLNKQLERGKIDGLKLA\r\nGVISTIHPTLDYAGFDRVDIVVEAVVENPKVKKAVLAETEQKVRQDTVLASNTSTIPISELANALERPENFCGMH\r\nFFNPVHRMPLVEIIRGEKSSDETIAKVVAWASKMGKTPIVVNDCPGFFVNRVLFPYFAGFSQLLRDGADFRKIDK\r\nVMEKQFGWPMGPAYLLDVVGIDTAHHAQAVMAAGFPQRMQKDYRDAIDALFDANRFGQKNGLGFWRYKEDSKGKP\r\nKKEEDAAVEDLLAEVSQPKRDFSEEEIIARMMIPMVNEVVRCLEEGIIATPAEADMALVYGLGFPPFHGGAFRWL\r\nDTLGSAKYLDMAQQYQHLGPLYEVPEGLRNKARHNEPYYPPVEPARPVGDLKTA",
"organism": "Escherichia coli",
"uniprot_code": "P21177",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MLYKGDTLYLDWLEDGIAELVFDAPGSVNKLDTATVASLGEAIGVLEQQSDLKGLLLRSN\nKAAFIVGADITEFLSLFLVPEEQLSQWLHFANSVFNRLEDLPVPTIAAVNGYALGGGCEC\nVLATDYRLATPDLRIGLPETKLGIMPGFGGSVRMPRMLGADSALEIIAAGKDVGADQALK\nIGLVDGVVKAEKLVEGAKAVLRQAINGDLDWKAKRQPKLEPLKLSKIEATMSFTIAKGMV\nAQTAGKHYPAPITAVKTIEAAARFGREEALNLENKSFVPLAHTNEARALVGIFLNDQYVK\nGKAKKLTKDVETPKQAAVLGAGIMGGGIAYQSAWKGVPVVMKDINDKSLTLGMTEAAKLL\nNKQLERGKIDGLKLAGVISTIHPTLDYAGFDRVDIVVEAVVENPKVKKAVLAETEQKVRQ\nDTVLASNTSTIPISELANALERPENFCGMHFFNPVHRMPLVEIIRGEKSSDETIAKVVAW\nASKMGKTPIVVNDCPGFFVNRVLFPYFAGFSQLLRDGADFRKIDKVMEKQFGWPMGPAYL\nLDVVGIDTAHHAQAVMAAGFPQRMQKDYRDAIDALFDANRFGQKNGLGFWRYKEDSKGKP\nKKEEDAAVEDLLAEVSQPKRDFSEEEIIARMMIPMVNEVVRCLEEGIIATPAEADMALVY\nGLGFPPFHGGAFRWLDTLGSAKYLDMAQQYQHLGPLYEVPEGLRNKARHNEPYYPPVEPA\nRPVGDLKTA",
"mw": 81.206,
"total_mw": 81.206,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "3-ketoacyl-CoA thiolase FadA (beta subunit)",
"short_name": "EcTFE-beta",
"sequence": ">EcTFE-beta\r\nMEQVVIVDAIRTPMGRSKGGAFRNVRAEDLSAHLMRSLLARNPALEAAALDDIYWGCVQQTLEQGFNIARNAALL\r\nAEVPHSVPAVTVNRLCGSSMQALHDAARMIMTGDAQACLVGGVEHMGHVPMSHGVDFHPGLSRNVAKAAGMMGLT\r\nAEMLARMHGISREMQDAFAARSHARAWAATQSAAFKNEIIPTGGHDADGVLKQFNYDEVIRPETTVEALATLRPA\r\nFDPVNGMVTAGTSSALSDGAAAMLVMSESRAHELGLKPRARVRSMAVVGCDPSIMGYGPVPASKLALKKAGLSAS\r\nDIGVFEMNEAFAAQILPCIKDLGLIEQIDEKINLNGGAIALGHPLGCSGARISTTLLNLMERKDVQFGLATMCIG\r\nLGQGIATVFERV",
"organism": "Escherichia coli",
"uniprot_code": "P21151",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MEQVVIVDAIRTPMGRSKGGAFRNVRAEDLSAHLMRSLLARNPALEAAALDDIYWGCVQQ\nTLEQGFNIARNAALLAEVPHSVPAVTVNRLCGSSMQALHDAARMIMTGDAQACLVGGVEH\nMGHVPMSHGVDFHPGLSRNVAKAAGMMGLTAEMLARMHGISREMQDAFAARSHARAWAAT\nQSAAFKNEIIPTGGHDADGVLKQFNYDEVIRPETTVEALATLRPAFDPVNGMVTAGTSSA\nLSDGAAAMLVMSESRAHELGLKPRARVRSMAVVGCDPSIMGYGPVPASKLALKKAGLSAS\nDIGVFEMNEAFAAQILPCIKDLGLIEQIDEKINLNGGAIALGHPLGCSGARISTTLLNLM\nERKDVQFGLATMCIGLGQGIATVFERV",
"mw": 40.876,
"total_mw": 81.752,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES), 120 mM KCl, 2.5 mM DTT",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.2,
"deuteration": null
},
"purity_method": null,
"name": "Escherichia coli aerobic fatty acid beta-oxidation trifunctional enzyme complex",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Finland",
"full_name": "University of Oulu",
"webpage": "https://www.oulu.fi"
}
],
"contributor_name": "shiv k.",
"contributor_surname": "sah-teli",
"orcid": ""
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-05-30",
"storage_temperature": 4.0,
"cell_temperature": 20.0,
"exposure_time": 3.0,
"number_of_frames": 540,
"wavelength": 0.1,
"sample_detector_distance": 4.014,
"concentration_min": null,
"concentration_max": 6.2,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.167,
"s_max": 1.913,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEL9_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/SASDEL9_fit1_model1.pdb",
"model_mw": 227.515,
"bead_radius": 5.8,
"log": "https://www.sasbdb.org/media/log_files/EcTFEdam.log",
"symmetry": "p1",
"comment": null,
"user": 400
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/EcTFEdam_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 1.029,
"p_value": 0.936796,
"fit_residual_plot": "EcTFEdam_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEL9_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/EcTFEdam.log",
"software_version": null,
"description": "we have used DAMMIN through online ATSAS package using the online cluster of EMBL, Hamburg, Germany"
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEL9_fit2_model1_img.png",
"software": "SwissModel",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEL9_fit2_model1.pdb",
"model_mw": 237.1,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "subunits and complex were modeled using swissmodel and coot respectively using 1wdm.pdb as referenc",
"user": 400
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/EcTFEmodelon1wdm00_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.357,
"p_value": 1e-06,
"fit_residual_plot": "EcTFEmodelon1wdm00_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEL9_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/EcTFEmodelon1wdm00.log",
"software_version": null,
"description": ""
}
],
"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 the E. coli aerobic fatty acid beta-oxidation trifunctional enzyme complex in 20 mM HEPES, 120 mM KCl, 2.5 mM DTT, pH 7.2 were measured at 20°C using size-exclusion chromatography SAXS (SEC-SAXS) on the B21 beam line at the Diamond Light Source (Oxfordshire, UK) using a Pilatus 2M detector at a sample-detector distance of 4.0 m and at a wavelength of λ = 0.1 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). The data were collected as 540 successive 3 second frames through the SEC elution profile (sample concentration = 6.20 mg/ml ). The SAXS data were measured from the sample and buffer from a Shodex KW403 column at flow rate of 0.16 mL/min. The sample-peak data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the individual subtracted data sets were scaled and averaged to generate the scattering profile displayed in this entry.",
"tags": [],
"intensity_unit": "1/cm",
"experimental_mw": 233.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 253.0,
"porod_mw_error": null,
"pddf_i0": 0.06542,
"pddf_i0_error": null,
"guinier_i0": 0.06559,
"guinier_i0_error": 0.0005,
"pddf_rg": 4.59,
"pddf_rg_error": null,
"guinier_rg": 4.612,
"guinier_rg_error": 0.04,
"pddf_dmax": 16.04,
"pddf_dmax_error": null,
"porod_volume": 406.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 51,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDEL9_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-11-09T18:33:41.024084+01:00",
"bragg_peak": []
}
