查看完整 summary.json 原文
{
"code": "SASDFA2",
"status": "Published",
"type_of_curve": "Extrapolated to infinite dilution",
"angular_unit": "1/nm",
"project": {
"title": "Did evolution create a flexible ligand-binding cavity in the urokinase receptor through deletion of a plesiotypic disulfide bond?",
"publication": {
"title": "Did evolution create a flexible ligand-binding cavity in the urokinase receptor through deletion of a plesiotypic disulfide bond?",
"author_list": "Leth JM, Mertens HDT, Leth-Espensen KZ, Jørgensen TJD, Ploug M",
"journal": "J Biol Chem",
"doi": "10.1074/jbc.RA119.007847",
"pmid": "30894413",
"published_date": "2019 Mar 20"
},
"status": "released",
"submitted_date": "2019-01-30",
"released_date": "2019-03-20"
},
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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",
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},
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"molecule": [
{
"long_name": "Urokinase plasminogen activator surface receptor",
"short_name": "uPAR",
"sequence": ">sp|Q03405|UPAR_HUMAN Urokinase plasminogen activator surface receptor OS=Homo sapiens GN=PLAUR PE=1 SV=1\nMGHPPLLPLLLLLHTCVPASWGLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEEL\nELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISC\nGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNG\nFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGP\nMNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDV\nQYRSGAAPQPGPAHLSLTITLLMTARLWGGTLLWT\n\n",
"organism": "Homo sapiens",
"uniprot_code": "Q03405",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MGHPPLLPLLLLLHTCVPASWGLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEEL\nELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISC\nGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNG\nFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGP\nMNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDV\nQYRSGAAPQPGPAHLSLTITLLMTARLWGGTLLWT",
"mw": 36.98,
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"number_molecules": 1,
"complex_state": null,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Urokinase-type plasminogen activator (Amino Terminal Fragment)",
"short_name": "ATF",
"sequence": "MRALLARLLL CVLVVSDSKG SNELHQVPSN CDCLNGGTCV SNKYFSNIHW \r\nCNCPKKFGGQ HCEIDKSKTC YEGNGHFYRG KASTDTMGRP CLPWNSATVL \r\nQQTYHAHRSD ALQLGLGKHN YCRNPDNRRR PWCYVQVGLK PLV",
"organism": "Homo sapiens",
"uniprot_code": "P00749",
"uniprot_range_first": 1,
"uniprot_range_last": 143,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MRALLARLLLCVLVVSDSKGSNELHQVPSNCDCLNGGTCVSNKYFSNIHWCNCPKKFGGQ\nHCEIDKSKTCYEGNGHFYRGKASTDTMGRPCLPWNSATVLQQTYHAHRSDALQLGLGKHN\nYCRNPDNRRRPWCYVQVGLKPLVQECMVHDCADGKKPSSPPEELKFQCGQKTLRPRFKII\nGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLG\nRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTICL\nPSMYNDPQFGTSCEITGFGKENSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKML\nCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIR\nSHTKEENGLAL",
"mw": 16.099,
"total_mw": 16.099,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
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"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.4,
"deuteration": null
},
"purity_method": null,
"name": "Urokinase plasminogen activator surface receptor, uPAR T51C-V70C, complex with urokinase-type plasminogen activator (Amino Terminal Fragment, ATF).",
"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": "2017-12-01",
"storage_temperature": 10.0,
"cell_temperature": 10.0,
"exposure_time": 0.05,
"number_of_frames": 20,
"wavelength": 0.124,
"sample_detector_distance": 3.1,
"concentration_min": 0.3,
"concentration_max": 2.5,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.086,
"s_max": 5.088,
"total_exposure_time": null,
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},
"fits": [
{
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{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFA2_fit1_model1_img.png",
"software": "DAMMIN",
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"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDFA2_fit1_model1.pdb",
"model_mw": 52.445,
"bead_radius": 2.75,
"log": "https://www.sasbdb.org/media/log_files/ref_pAy50hf.log",
"symmetry": null,
"comment": "Refined DAMMIN model from average volume (10 DAMMIF iterations)",
"user": 12
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/ref_VT6nwiZ_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 1.26,
"p_value": 0.490943,
"fit_residual_plot": "ref_VT6nwiZ_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFA2_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/ref_zjiGKjj.log",
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}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
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"i0_calibration_standard": null,
"description": "Introduced disulfide in the first LU domain, DI, of uPAR (T51C-V70C).",
"experiment_description": "Synchrotron SAXS data from solutions of uPAR T51C-V70C in complex with uPA-ATF in 20 mM PBS, 5 %(v/v) glycerol, pH 7.4 were collected on the EMBL P12 beam line at PETRA III (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3.1 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.3 and 2.5 mg/ml were measured at 10°C. 20 successive 0.050 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. The low angle data collected at lower concentrations were extrapolated to infinite dilution and merged with the higher concentration data to yield the final composite scattering curve.",
"tags": [],
"intensity_unit": "1/cm",
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"pddf_dmax": 8.5,
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"porod_volume": 77.1,
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"estimated_volume": null,
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"guinier_point_first": 1,
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"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDFA2_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}查看完整 manifest.json 原文
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