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": "SASDFD6",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/nm",
"project": {
"title": "Studying Conformational Changes of the Yersinia Type-III-Secretion Effector YopO in Solution by Integrative Structural Biology.",
"publication": {
"title": "Studying Conformational Changes of the Yersinia Type-III-Secretion Effector YopO in Solution by Integrative Structural Biology.",
"author_list": "Peter MF, Tuukkanen AT, Heubach CA, Selsam A, Duthie FG, Svergun DI, Schiemann O, Hagelueken G",
"journal": "Structure",
"doi": "10.1016/j.str.2019.06.007",
"pmid": "31303480",
"published_date": "2019 Sep 3"
},
"status": "released",
"submitted_date": "2019-05-06",
"released_date": "2019-09-11"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFD6.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFD6.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFD6_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFD6_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFD6_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFD6_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFD6.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"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,
"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": "Protein kinase YopO",
"short_name": "YopO",
"sequence": "KPQTELPLGWKGKPLSGAPDLEGMRVAHISIIERLVAKIGHLFAELEAYKHIYKTAGKHPNLANVHGMAVVPYGNRYYYALLMDEVDGWRCSDTLRSLADSWKQGKINSEAYWGTIKFIAHRLLDVTNHLAKAGIVHNDIKPGNVVFDRASGEPVVIDLGLHSRSGEQPKGFTESFKAPELGVGGASEKSDVFLVVSTLLHGIEGFEKDPEIKPNQGLRFITSEPAHVMDENGYPIHRPGIAGVETAYTRFITDILGVSADSRPDSNEARLHEFLSDGTIDEESAKQILKDTLTGEMSITPYYLRELSDLLRTHLSSAATKQLDMGVVLSDLDTMLVALDKAEREGGVDKDQLKSFNSLILKTYSVIGAYILSIVEPSLQRIQKHLDQTHSFSDIGSLMRAHKHLETLLEVLVTLSQQGQPVSSETYSFLNRLAEAKVTLSQQLNTLQQQQESAKAQLSILINRSGSWADVARQSLQRFDSTRPVVKFGTEQYTAIHRQMMAAHAAITLQEVSEFTDDMRNFTADSIPLLIQLGRSSLMDEHLVEQREKLRELTTIAERLNRLEREWM",
"organism": "Yersinia enterocolitica",
"uniprot_code": "Q93KQ6",
"uniprot_range_first": 89,
"uniprot_range_last": 729,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MKIMGTMSPSISLAKAHERISKHWQNPVGELNIEGKRYRIIDNQVLRLNPHSGFSLFREG\nVGKIFSGKMFSFSIARNLTDTLHAAQKTTSQELRSDIPNALSNLFGAKPQTELPLGWKGK\nPLSGAPDLEGMRVAETDKFAEGESHISIIETKDKQRLVAKIERSIAEGHLFAELEAYKHI\nYKTAGKHPNLANVHGMAVVPYGNRKEEALLMDEVDGWRCSDTLRSLADSWKQGKINSEAY\nWGTIKFIAHRLLDVTNHLAKAGIVHNDIKPGNVVFDRASGEPVVIDLGLHSRSGEQPKGF\nTESFKAPELGVGNLGASEKSDVFLVVSTLLHGIEGFEKDPEIKPNQGLRFITSEPAHVMD\nENGYPIHRPGIAGVETAYTRFITDILGVSADSRPDSNEARLHEFLSDGTIDEESAKQILK\nDTLTGEMSPLPTDVRRITPKKLRELSDLLRTHLSSAATKQLDMGVVLSDLDTMLVALDKA\nEREGGVDKDQLKSFNSLILKTYSVIGAYIKGREGDTKSSSTEVSPYHRSNFMLSIVEPSL\nQRIQKHLDQTHSFSDIGSLMRAHKHLETLLEVLVTLSQQGQPVSSETYSFLNRLAEAKVT\nLSQQLNTLQQQQESAKAQLSILINRSGSWADVARQSLQRFDSTRPVVKFGTEQYTAIHRQ\nMMAAHAAITLQEVSEFTDDMRNFTADSIPLLIQLGRSSLMDEHLVEQREKLRELTTIAER\nLNRLEREWM",
"mw": 63.387,
"total_mw": 63.387,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Actin, cytoplasmic 1",
"short_name": "Actin",
"sequence": "MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS\r\nKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT\r\nQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL\r\nAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY\r\nELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLS\r\nGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ\r\nEYDESGPSIVHRKCF",
"organism": "Homo sapiens",
"uniprot_code": "P60709",
"uniprot_range_first": 1,
"uniprot_range_last": 375,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS\nKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT\nQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL\nAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY\nELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLS\nGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ\nEYDESGPSIVHRKCF",
"mw": 41.737,
"total_mw": 41.737,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "10 mM Tris-HCl, 50 mM NaCl",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 8.0,
"deuteration": null
},
"purity_method": null,
"name": "Protein kinase YopO - cytoplasmic 1 actin complex",
"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": "Anne",
"contributor_surname": "Tuukkanen",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-05-06",
"storage_temperature": 10.0,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 3600,
"wavelength": 0.124,
"sample_detector_distance": 3.0,
"concentration_min": null,
"concentration_max": 5.52,
"sample_volume": 80.0,
"flow_rate": null,
"s_min": 0.133,
"s_max": 7.267,
"total_exposure_time": null,
"seccolumn": 1
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFD6_fit1_model1_img.png",
"software": "Custom in-house",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDFD6_fit1_model1.pdb",
"model_mw": 103.5,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "PELDOR/SAXS refinement without clash penalty",
"user": 27
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/617currentBest_000_n21qnQr_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.098,
"p_value": 0.01337,
"fit_residual_plot": "617currentBest_000_n21qnQr_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFD6_fit1.fit",
"fit_log": null,
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFD6_fit2_model1_img.png",
"software": "Custom in-house",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDFD6_fit2_model1.pdb",
"model_mw": 103.5,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "PELDOR/SAXS refinement with clash penalty",
"user": 27
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/616_currentBest_000_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.123,
"p_value": 0.003355,
"fit_residual_plot": "616_currentBest_000_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFD6_fit2.fit",
"fit_log": null,
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"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFD6_fit3_model1_img.png",
"software": "Custom in-house",
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"model_title": null,
"type_of_model": "atomic",
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"model_data": "https://www.sasbdb.org/media/pdb_file/SASDFD6_fit3_model1.pdb",
"model_mw": 103.5,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "Model ignoring the Kinase 113 – Actin 374 restraint",
"user": 27
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/621_currentBest_000_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.075,
"p_value": 0.01337,
"fit_residual_plot": "621_currentBest_000_fitresiduals_img.png",
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"fit_log": null,
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"description": ""
}
],
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"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of protein kinase YopO in complex with actin in 10 mM Tris-HCl, 50 mM NaCl, pH 8 were collected on the EMBL P12 beam line at the PETRA III (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAXS was employed. The SEC parameters were as follows: A 80.00 μl sample at 5.5 mg/ml was injected onto a GE Superdex 200 Increase 10/300 column at 20°C. 3600 successive 1 second frames were collected through the SEC elution. The data from the sample peak were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 109.1,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 82.1,
"porod_mw_error": null,
"pddf_i0": 615.1,
"pddf_i0_error": 3.1,
"guinier_i0": 611.0,
"guinier_i0_error": 1.0,
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"guinier_rg": 3.6,
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"pddf_dmax": 12.33,
"pddf_dmax_error": 0.6,
"porod_volume": 147.0,
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"estimated_volume": null,
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"guinier_point_first": 1,
"guinier_point_last": 84,
"pddf_point_first": null,
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"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDFD6_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}
