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": "SASDDS9",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/nm",
"project": {
"title": "Human MICAL1: activation by the small GTPase Rab8 and small-angle X-ray scattering studies on the oligomerization state of MICAL1 and its complex with Rab8.",
"publication": {
"title": "Human MICAL1: activation by the small GTPase Rab8 and small-angle X-ray scattering studies on the oligomerization state of MICAL1 and its complex with Rab8.",
"author_list": "Esposito A, Ventura V, Petoukhov MV, Rai A, Svergun DI, Vanoni MA",
"journal": "Protein Sci",
"doi": "10.1002/pro.3512",
"pmid": "30242933",
"published_date": "2018 Sep 22"
},
"status": "released",
"submitted_date": "2018-07-17",
"released_date": "2018-09-25"
},
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"experiment": {
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"name": "Pilatus 2M",
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},
"name": "PETRA III",
"city": "DESY; Hamburg",
"country": "Germany",
"beamline_name": "EMBL P12",
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"type_of_source": "X-ray synchrotron",
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},
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{
"long_name": "[F-actin]-monooxygenase MICAL1 (MoChLim)",
"short_name": "MoChLim",
"sequence": "MASPTSTNPAHAHFESFLQAQLCQDVLSSFQELCGALGLEPGGGLPQYHKIKDQLNYWSAKSLW\r\nTKLDKRAGQPVYQQGRACTSTKCLVVGAGPCGLRVAVELALLGARVVLVEKRTKFSRHNVLHLW\r\nPFTIHDLRALGAKKFYGRFCTGTLDHISIRQLQLLLLKVALLLGVEIHWGVTFTGLQPPPRKGS\r\nGWRAQLQPNPPAQLANYEFDVLISAAGGKFVPEGFKVREMRGKLAIGITANFVNGRTVEETQVP\r\nEISGVARIYNQSFFQSLLKATGIDLENIVYYKDDTHYFVMTAKKQCLLRLGVLRQDWPDTNRLL\r\nGSANVVPEALQRFTRAAADFATHGKLGKLEFAQDAHGQPDVSAFDFTSMMRAESSARVQEKHGA\r\nRLLLGLVGDCLVEPFWPLGTGVARGFLAAFDAAWMVKRWAEGAESLEVLAERESLYQLLSQTSP\r\nENMHRNVAQYGLDPATRYPNLNLRAVTPNQVRDLYDVLAKEPVQRNNDKTDTGMPATGSAGTQE\r\nELLRWCQEQTAGYPGVHVSDLSSSWADGLALCALVYRLQPGLLEPSELQGLGALEATAWALKVA\r\nENELGITPVVSAQAVVAGSDPLGLIAYLSHFHSAFKSMAHSPGPVSQASPGTSSAVLFLSKLQR\r\nTLQRSRAKENAEDAGGKKLRLEMEAETPSTEVPPDPEPGVPLTPPSQHQEAGAGDLCALCGEHL\r\nYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQTDHKKEGSDRGPESP\r\nELPTPSENSM",
"organism": "Homo sapiens",
"uniprot_code": "Q8TDZ2",
"uniprot_range_first": 1,
"uniprot_range_last": 778,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MASPTSTNPAHAHFESFLQAQLCQDVLSSFQELCGALGLEPGGGLPQYHKIKDQLNYWSA\nKSLWTKLDKRAGQPVYQQGRACTSTKCLVVGAGPCGLRVAVELALLGARVVLVEKRTKFS\nRHNVLHLWPFTIHDLRALGAKKFYGRFCTGTLDHISIRQLQLLLLKVALLLGVEIHWGVT\nFTGLQPPPRKGSGWRAQLQPNPPAQLANYEFDVLISAAGGKFVPEGFKVREMRGKLAIGI\nTANFVNGRTVEETQVPEISGVARIYNQSFFQSLLKATGIDLENIVYYKDDTHYFVMTAKK\nQCLLRLGVLRQDWPDTNRLLGSANVVPEALQRFTRAAADFATHGKLGKLEFAQDAHGQPD\nVSAFDFTSMMRAESSARVQEKHGARLLLGLVGDCLVEPFWPLGTGVARGFLAAFDAAWMV\nKRWAEGAESLEVLAERESLYQLLSQTSPENMHRNVAQYGLDPATRYPNLNLRAVTPNQVR\nDLYDVLAKEPVQRNNDKTDTGMPATGSAGTQEELLRWCQEQTAGYPGVHVSDLSSSWADG\nLALCALVYRLQPGLLEPSELQGLGALEATAWALKVAENELGITPVVSAQAVVAGSDPLGL\nIAYLSHFHSAFKSMAHSPGPVSQASPGTSSAVLFLSKLQRTLQRSRAKENAEDAGGKKLR\nLEMEAETPSTEVPPDPEPGVPLTPPSQHQEAGAGDLCALCGEHLYVLERLCVNGHFFHRS\nCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQTDHKAEGSDRGPESPELPTPSENSMPP\nGLSTPTASQEGAGPVPDPSQPTRRQIRLSSPERQRLSSLNLTPDPEMEPPPKPPRSCSAL\nARHALESSFVGWGLPVQSPQALVAMEKEEKESPFSSEEEEEDVPLDSDVEQALQTFAKTS\nGTMNNYPTWRRTLLRRAKEEEMKRFCKAQTIQRRLNEIEAALRELEAEGVKLELALRRQS\nSSPEQQKKLWVGQLLQLVDKKNSLVAEEAELMITVQELNLEEKQWQLDQELRGYMNREEN\nLKTAADRQAEDQVLRKLVDLVNQRDALIRFQEERRLSELALGTGAQG",
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"total_mw": 85.162,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
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"concentration_unit": null,
"comment": "MoChLim buffer",
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "NADPH oxidase (H2O2 producing and [F-actin] oxidizing) MICAL1 (monomer) (Truncated MOCHLIM construct)",
"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": "Maxim",
"contributor_surname": "Petoukhov",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-06-20",
"storage_temperature": 23.0,
"cell_temperature": 10.0,
"exposure_time": 1.0,
"number_of_frames": 3600,
"wavelength": 0.124,
"sample_detector_distance": 3.0,
"concentration_min": null,
"concentration_max": 6.82,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.144,
"s_max": 5.035,
"total_exposure_time": null,
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},
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"software": "CORAL",
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"model_title": null,
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"software_version": null,
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"model_mw": 117.5,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": "PDB file corresponds to full-length Mical1",
"user": 102
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDS9_fit1_fit_img.png",
"software": "CORAL",
"chi_square_value": 1.63,
"p_value": 0.0,
"fit_residual_plot": "SASDDS9_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDS9_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/cor04_TaWP0eh.log",
"software_version": null,
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}
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"pddf_software": "ATSAS GNOM",
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"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data, I(s) vs s (where s = 4πsinθ/λ, and 2θ is the scattering angle), were measured from the MoChLim construct of MICAL1 using continuous-flow size-exclusion chromatography SAXS (SEC-SAXS) on the EMBL-P12 beam line at the PETRA III storage ring (Hamburg, Germany). Data were collected a using a Pilatus 2M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm. The SEC mobile phase (0.5 ml/min) consisted of 20 mM Hepes/NaOH, pH 7.5, 50 mM NaCl, 2 mM MgCl2, 2 mM DTT, pH 7.5 (23°C). The sample load concentration onto the SEC column was 6.82 mg/ml (90 µl injection volume). The SAXS data measured from the SEC-elution (sample peak and buffer; 3600 successive 1 s frames) were normalized to the intensity of the transmitted beam and radially averaged. The scattering of an appropriate solvent-blank was subtracted from the sample frames to produce the scaled and averaged data displayed in this entry.",
"tags": [],
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"porod_volume": 145.0,
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"estimated_volume": null,
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"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDDS9_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}View the complete manifest.json source
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