full_entry_zip：来源记录与 ZIP 内部目录（11 项）
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}查看完整 summary.json 原文
{
"code": "SASDB95",
"status": "Published",
"type_of_curve": "Other",
"angular_unit": "1/nm",
"project": {
"title": "The Shigella Virulence Factor IcsA Relieves N-WASP Autoinhibition by Displacing the Verprolin Homology/Cofilin/Acidic (VCA) Domain.",
"publication": {
"title": "The Shigella Virulence Factor IcsA Relieves N-WASP Autoinhibition by Displacing the Verprolin Homology/Cofilin/Acidic (VCA) Domain.",
"author_list": "Mauricio RP, Jeffries CM, Svergun DI, Deane JE",
"journal": "J Biol Chem",
"doi": "10.1074/jbc.M116.758003",
"pmid": "27881679",
"published_date": "2017 Jan 6"
},
"status": "released",
"submitted_date": "2016-08-17",
"released_date": "2016-11-24"
},
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"experiment": {
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"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,
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},
"sample": {
"molecule": [
{
"long_name": "Outer membrane protein IcsA (53-758)",
"short_name": "IcsA",
"sequence": "TPLSGTQELHFSEDNYEKLLTPVDGLSPLGAGEDGMDAWYITSSNPSH\r\nASRTKLRINSDIMISAGHGGAGDNNDGNSCGGNGGDSITGSDLSIINQGM\r\nILGGSGGSGADHNGDGGEAVTGDNLFIINGEIISGGHGGDSYSDSDGGNG\r\nGDAVTGVNLPIINKGTISGGNGGNNYGEGDGGNGGDAITGSSLSVINKGT\r\nFAGGNGGAAYGYGYDGYGGNAITGDNLSVINNGAILGGNGGHWGDAINGS\r\nNMTIANSGYIISGKEDDGTQNVAGNAIHITGGNNSLILHEGSVITGDVQV\r\nNNSSILKIINNDYTGTTPTIEGDLCAGDCTTVSLSGNKFTVSGDVSFGEN\r\nSSLNLAGISSLEASGNMSFGNNVKVEAIINNWAQKDYKLLSADKGITGFS\r\nVSNISIINPLLTTGAIDYTKSYISDQNKLIYGLSWNDTDGDSHGEFNLKE\r\nNAELTVSTILADNLSHHNINSWDGKSLTKSGEGTLILAEKNTYSGFTNIN\r\nAGILKMGTVEAMTRTAGVIVNKGATLNFSGMNQTVNTLLNSGTVLINNIN\r\nAPFLPDPVIVTGNMTLEKNGHVILNNSSSNVGQTYVQKGNWHGKGGILSL\r\nGAVLGNDNSKTDRLEIAGHASGITYVAVTNEGGSGDKTLEGVQIISTDSS\r\nDKNAFIQKGRIVAGSYDYRLKQGTVSGLNTNKWYLTSQMDNQESKQMSNQ\r\nESTQMSSR",
"organism": "Shigella flexneri",
"uniprot_code": "Q7BCK4",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MNQIHKFFCNMTQCSQGGAGELPTVKEKTCKLSFSPFVVGASLLLGGPIAFATPLSGTQE\nLHFSEDNYEKLLTPVDGLSPLGAGEDGMDAWYITSSNPSHASRTKLRINSDIMISAGHGG\nAGDNNDGNSCGGNGGDSITGSDLSIINQGMILGGSGGSGADHNGDGGEAVTGDNLFIING\nEIISGGHGGDSYSDSDGGNGGDAVTGVNLPIINKGTISGGNGGNNYGEGDGGNGGDAITG\nSSLSVINKGTFAGGNGGAAYGYGYDGYGGNAITGDNLSVINNGAILGGNGGHWGDAINGS\nNMTIANSGYIISGKEDDGTQNVAGNAIHITGGNNSLILHEGSVITGDVQVNNSSILKIIN\nNDYTGTTPTIEGDLCAGDCTTVSLSGNKFTVSGDVSFGENSSLNLAGISSLEASGNMSFG\nNNVKVEAIINNWAQKDYKLLSADKGITGFSVSNISIINPLLTTGAIDYTKSYISDQNKLI\nYGLSWNDTDGDSHGEFNLKENAELTVSTILADNLSHHNINSWDGKSLTKSGEGTLILAEK\nNTYSGFTNINAGILKMGTVEAMTRTAGVIVNKGATLNFSGMNQTVNTLLNSGTVLINNIN\nAPFLPDPVIVTGNMTLEKNGHVILNNSSSNVGQTYVQKGNWHGKGGILSLGAVLGNDNSK\nTDRLEIAGHASGITYVAVTNEGGSGDKTLEGVQIISTDSSDKNAFIQKGRIVAGSYDYRL\nKQGTVSGLNTNKWYLTSQMDNQESKQMSNQESTQMSSRRASSQLVSSLNLGEGSIHTWRP\nEAGSYIANLIAMNTMFSPSLYDRHGSTIVDPTTGQLSETTMWIRTVGGHNEHNLADRQLK\nTTANRMVYQIGGDILKTNFTDHDGLHVGIMGAYGYQDSKTHNKYTSYSSRGTVSGYTAGL\nYSSWFQDEKERTGLYMDAWLQYSWFNNTVKGDGLTGEKYSSKGITGALEAGYIYPTIRWT\nAHNNIDNALYLNPQVQITRHGVKANDYIEHNGTMVTSSGGNNIQAKLGLRTSLISQSCID\nKETLRKFEPFLEVNWKWSSKQYGVIMNGMSNHQIGNRNVIELKTGVGGRLADNLSIWGNV\nSQQLGNNSYRDTQGILGVKYTF",
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"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
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"name": "50 mM Tris 150 mM NaCl 10 mM CaCl2 3% v/v glycerol",
"concentration_unit": "mM",
"comment": null,
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"concentration": 50.0,
"pka": null,
"ph": 7.4,
"deuteration": null
},
"purity_method": null,
"name": "Shigella outer membrane protein IcsA autotransporter",
"ext_coefficient": null,
"contrast": null,
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"dry_vol": null,
"absorbption": null,
"deuteration": null,
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},
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{
"affiliation": [
{
"short_name": "CIMR",
"address": "Cambridge, UK",
"full_name": "Cambridge Institute for Medical Research , Department of Pathology, University of Cambridge",
"webpage": "http://www.cimr.cam.ac.uk/"
}
],
"contributor_name": "Janet",
"contributor_surname": "Deane",
"orcid": null
},
{
"affiliation": [
{
"short_name": "EMBL-Hamburg",
"address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
"full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
"webpage": "http://www.embl-hamburg.de/index.php"
}
],
"contributor_name": "Cy M",
"contributor_surname": "Jeffries",
"orcid": null
},
{
"affiliation": [
{
"short_name": "CIMR",
"address": "Cambridge, UK",
"full_name": "Cambridge Institute for Medical Research , Department of Pathology, University of Cambridge",
"webpage": "http://www.cimr.cam.ac.uk/"
}
],
"contributor_name": "Rui",
"contributor_surname": "Mauricio",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2016-05-18",
"storage_temperature": 20.0,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 119,
"wavelength": 0.124,
"sample_detector_distance": 3.1,
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"concentration_max": null,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.076,
"s_max": 3.009,
"total_exposure_time": null,
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},
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"type_of_model": "dummy",
"software_version": "",
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"bead_radius": 3.4,
"log": "https://www.sasbdb.org/media/log_files/IcsA1a.log",
"symmetry": "",
"comment": "",
"user": 9
}
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"fit_unit": "1/A",
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"software": null,
"chi_square_value": 1.858,
"p_value": 0.841,
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}
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"pddf_software": "ATSAS GNOM",
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"description": "The bead models displayed for IcsA are individual/representative low-resolution structural examples calculated using DAMMIN or GASBOR. A cohort of individual GASBOR and DAMMIN models are supplied in the full entry zip archive and include the average DAMMIN-based spatial representation of IcsA in solution (damfilt.pdb; NSD = 0.7).\r\nIndividual reduced SEC-SAXS data frames/blocks and Rg/I(0) analysis through the IcsA elution peak are included in the full entry zip archive.",
"experiment_description": "Synchrotron SAXS data from solutions of Shigella flexneri outer membrane protein IcsA (53–758) in 50 mM Tris, 150 mM NaCl, 10 mM CaCl2, 3% v/v glycerol, pH 7.4 were collected using size-exclusion chromatography (SEC) SAXS on the EMBL-P12 bioSAXS beam line at the PETRAIII storage ring (Hamburg, Germany) equipped with a Pilatus 2M detector (I(s) vs s, where s = 4π sin θ/λ; 2θ is the scattering angle; λ = 0.124 nm). 119 successive 1 second frames were collected through the monomeric IcsA SEC elution peak (GE Healthcare Life Sciences Superdex 200 Increase column; 0.4 ml/min; 75 μl injection at 8 mg/ml). The data were normalised to the intensity of the transmitted beam and the scattering of the solvent-blank (derived from 50 x 1 s data frames of pure, macromolecular free solvent) was subtracted. The resulting scattering profiles were scaled relative to each other (CorMap p > 0.01) then averaged to produce the final averaged IcsA SAXS data displayed in this entry.",
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"pddf_rg": 3.76,
"pddf_rg_error": 0.02,
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"guinier_rg_error": 0.02,
"pddf_dmax": 13.22,
"pddf_dmax_error": null,
"porod_volume": 103.0,
"porod_volume_error": null,
"estimated_volume": null,
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"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}
