The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
Every source field is expanded here, including empty values, list members and fields already shown above.
View the complete summary.json source
{
"code": "SASDBE7",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "Structure of the mycobacterial ESX-5 type VII secretion system membrane complex by single-particle analysis.",
"publication": {
"title": "Structure of the mycobacterial ESX-5 type VII secretion system membrane complex by single-particle analysis.",
"author_list": "Beckham KS, Ciccarelli L, Bunduc CM, Mertens HD, Ummels R, Lugmayr W, Mayr J, Rettel M, Savitski MM, Svergun DI, Bitter W, Wilmanns M, Marlovits TC, Parret AH, Houben EN",
"journal": "Nat Microbiol",
"doi": "10.1038/nmicrobiol.2017.47",
"pmid": "28394313",
"published_date": "2017 Apr 10"
},
"status": "released",
"submitted_date": "2016-11-04",
"released_date": "2016-11-04"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBE7.out",
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"experiment": {
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"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,
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},
"sample": {
"molecule": [
{
"long_name": "ESX-5 type VII secretion system protein EccC5",
"short_name": "EccC5",
"sequence": "KLDAMRAQFMLMLDMLRETAQESADSMDANYRWFHPAPTTLA\r\nAAVGSSRMWERQPDGKDLNFGVVRVGVGMTRPEVTWGEPQNMPTDIELEPVTGKALQEFGRYQSVVYNLP\r\nKMVSLLVEPWYSLVGEREQVLGLTRAIICQLAFSHGPDHVQMIVVTSDPDRWDWVKWIPHFGDPRRRDAA\r\nGNARMVYTSVREFATEQAELFAGRGSFTPRHASSSAETPTPHHVIISDIEDPQWEYVISSEGVDGVTFFD\r\nLTGSPLWTGAPQRVLRFTDSAGVIETLPRDRDTWMVIDDNAWFFALADQMSEADAEQFAHQMAHWRLAEA\r\nYEEIGQRVVQLGARDILSYYGIDDAGEIDFNTLWSGSGRRDLLSRSRLRIPFGNRADNGELLFLDMKSLD\r\nEGGDGPHGVMSGTTGSGKSSLVRTVIASLMLAHPPEELQFVLADLKGGSAVKPFDGVPHVSRIITDLEDD\r\nQALMERFLEAMWGEIARRKEICFSAGVDGAKEYNELRARMKARGEDMPPLPMLVVVIDEFYEWFRIMPTA\r\nVDVLDSIGRQGRAYWVHLMMASQTIESRAEKLMENMGYRLVLKAQTAGAAQAAGVPNAVNLPSQAGLGYF\r\nRKSGDEIIRFQAEYLWRDYRRGSSYDGEEQAPLTHSVDYIRPQLFTTAFAPLEVSVSGPDGQSALPQVVD\r\nGEAVNGHRGGDDVDEEEEALRTPKVGTVIIDQLRQIDFEPYRLWHPPLDVPVPIDELVNRFLGRPWQQDY\r\nGTAKNLVFPIGIIDRPYKHDQPPWTVDTSGAGANVLILGAGGAGKTTALQTLICAAALTHTPEQVQFYCL\r\nAYSGTALTTVANLPHVGGVSGPTDPYGVRRTVAEVLGLVRDRKRSFLEYDVPSMEVFRRRKFGGEPGGVP\r\nDDGFGDVYLVIDNYRALAEENEVLIEQVNQIINQGPSFGVHVVATADRESELRPPVRSGFGSRVELRLAA\r\nVEDAKLVRSRFAKDVPPKPGRGMVAVNYVRLDSDPQAGLHTLVARPALGSTPDAVFESDSVAAAVRQVAA\r\nGEARPVRRLPARFGLDQLRQVAAADRRQGVGAGGIAWAISELDLQPVYLNFADNAHLMVTGRRECGRTTT\r\nLATIMSEIGRIYAPGASTAPPTSRPSAQVWLVDPRRQLLTVLGSDYVEKFAYNLDGVAAMMDDLAAALAR\r\nREPPPGLSAEELLSRSWWSGPEIFLIIDDIQQLPPGFDSPLHKAAPWVTRAADVGLHVFVTRTFGGWSSA\r\nGSDPILRALHQANAPLLVMDADPDEGFIRGKMKGGPLPRGRGLLMAEDTGVFVQVAATDLRR",
"organism": "Mycobacterium xenopi RIVM700367",
"uniprot_code": "I0RZI0",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MKQGFARPTPERAPVVKPENIVLPTPLSVPPPEGKPWWLVVVGVLVVGLLVGMVGMTVAS\nGSRLFLGAGAIFPIFMIGGVAMMMFGGRFGGQQQMSRPKLDAMRAQFMLMLDMLRETAQE\nSADSMDANYRWFHPAPTTLAAAVGSSRMWERQPDGKDLNFGVVRVGVGMTRPEVTWGEPQ\nNMPTDIELEPVTGKALQEFGRYQSVVYNLPKMVSLLVEPWYSLVGEREQVLGLTRAIICQ\nLAFSHGPDHVQMIVVTSDPDRWDWVKWIPHFGDPRRRDAAGNARMVYTSVREFATEQAEL\nFAGRGSFTPRHASSSAETPTPHHVIISDIEDPQWEYVISSEGVDGVTFFDLTGSPLWTGA\nPQRVLRFTDSAGVIETLPRDRDTWMVIDDNAWFFALADQMSEADAEQFAHQMAHWRLAEA\nYEEIGQRVVQLGARDILSYYGIDDAGEIDFNTLWSGSGRRDLLSRSRLRIPFGNRADNGE\nLLFLDMKSLDEGGDGPHGVMSGTTGSGKSSLVRTVIASLMLAHPPEELQFVLADLKGGSA\nVKPFDGVPHVSRIITDLEDDQALMERFLEAMWGEIARRKEICFSAGVDGAKEYNELRARM\nKARGEDMPPLPMLVVVIDEFYEWFRIMPTAVDVLDSIGRQGRAYWVHLMMASQTIESRAE\nKLMENMGYRLVLKAQTAGAAQAAGVPNAVNLPSQAGLGYFRKSGDEIIRFQAEYLWRDYR\nRGSSYDGEEQAPLTHSVDYIRPQLFTTAFAPLEVSVSGPDGQSALPQVVDGEAVNGHRGG\nDDVDEEEEALRTPKVGTVIIDQLRQIDFEPYRLWHPPLDVPVPIDELVNRFLGRPWQQDY\nGTAKNLVFPIGIIDRPYKHDQPPWTVDTSGAGANVLILGAGGAGKTTALQTLICAAALTH\nTPEQVQFYCLAYSGTALTTVANLPHVGGVSGPTDPYGVRRTVAEVLGLVRDRKRSFLEYD\nVPSMEVFRRRKFGGEPGGVPDDGFGDVYLVIDNYRALAEENEVLIEQVNQIINQGPSFGV\nHVVATADRESELRPPVRSGFGSRVELRLAAVEDAKLVRSRFAKDVPPKPGRGMVAVNYVR\nLDSDPQAGLHTLVARPALGSTPDAVFESDSVAAAVRQVAAGEARPVRRLPARFGLDQLRQ\nVAAADRRQGVGAGGIAWAISELDLQPVYLNFADNAHLMVTGRRECGRTTTLATIMSEIGR\nIYAPGASTAPPTSRPSAQVWLVDPRRQLLTVLGSDYVEKFAYNLDGVAAMMDDLAAALAR\nREPPPGLSAEELLSRSWWSGPEIFLIIDDIQQLPPGFDSPLHKAAPWVTRAADVGLHVFV\nTRTFGGWSSAGSDPILRALHQANAPLLVMDADPDEGFIRGKMKGGPLPRGRGLLMAEDTG\nVFVQVAATDLRR",
"mw": 142.453,
"total_mw": 142.453,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Tris 200 mM NaCl 5%(v/v) Glycerol",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 8.0,
"deuteration": null
},
"purity_method": null,
"name": "ESX-5 type VII secretion system protein EccC5",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"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": "Haydyn",
"contributor_surname": "Mertens",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2016-07-15",
"storage_temperature": 10.0,
"cell_temperature": 20.0,
"exposure_time": 0.045,
"number_of_frames": 20,
"wavelength": 0.124,
"sample_detector_distance": 3.3,
"concentration_min": null,
"concentration_max": 0.39,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.025,
"s_max": 5.031,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
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"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/logFile_001_1_PPLCUuX.log",
"symmetry": "P1",
"comment": "Ensemble member of EOM selected",
"user": 12
},
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],
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"p_value": 0.9,
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"fit_log": null,
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},
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"model_mw": 170.875,
"bead_radius": 5.0,
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"symmetry": "P1",
"comment": "DAMMIF models refined in DAMMIN",
"user": 12
}
],
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"software": "DAMMIN",
"chi_square_value": 0.946,
"p_value": 0.24,
"fit_residual_plot": "SASDBE7_fit2_fitresiduals_img.png",
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}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "GNOM (5.0)",
"i0_calibration_standard": null,
"description": "Note: The data set presented in this entry was measured from is single fraction from an offline size-exclusion chromatography (SEC) purification.",
"experiment_description": "Synchrotron SAXS data from solutions of ESX-5 type VII secretion system protein EccC5 in 20 mM Tris 200 mM NaCl 5% (v/v) glycerol, pH 8, were collected at the EMBL-P12 bioSAXS beam line on the PETRA-III storage ring (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3.3 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4π sin θ/λ, and 2θ is the scattering angle). A solute concentration of 0.4 mg/ml was measured at 20°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 and the resulting subtracted profile normalized to protein concentration.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 141.0,
"experimental_mw_error": null,
"guinier_i0_mw": 141.0,
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"porod_mw": 159.0,
"porod_mw_error": null,
"pddf_i0": 0.108,
"pddf_i0_error": 0.001,
"guinier_i0": 0.107,
"guinier_i0_error": 0.001,
"pddf_rg": 6.5,
"pddf_rg_error": 1.0,
"guinier_rg": 6.22,
"guinier_rg_error": 1.0,
"pddf_dmax": 23.0,
"pddf_dmax_error": 0.5,
"porod_volume": 255.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 23,
"guinier_point_last": 61,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDBE7_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}
