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": "SASDCK9",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Calmodulin fishing with a structurally disordered bait triggers CyaA catalysis.",
"publication": {
"title": "Calmodulin fishing with a structurally disordered bait triggers CyaA catalysis.",
"author_list": "O'Brien DP, Durand D, Voegele A, Hourdel V, Davi M, Chamot-Rooke J, Vachette P, Brier S, Ladant D, Chenal A",
"journal": "PLoS Biol",
"doi": "10.1371/journal.pbio.2004486",
"pmid": "29287065",
"published_date": "2017 Dec"
},
"status": "released",
"submitted_date": "2017-11-28",
"released_date": "2018-01-03"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDCK9.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCK9.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCK9_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCK9_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCK9_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCK9_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCK9.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "CCD",
"name": "AVIEX PCCD170170",
"resolution": null
},
"name": "SOLEIL",
"city": "Saint-Aubin",
"country": "France",
"beamline_name": "SWING",
"beam_geometry": "",
"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": "Bifunctional hemolysin/adenylate cyclase",
"short_name": "AC domain from CyaA",
"sequence": "MQQSHQAGYANAADRESGIPAAVLDGIKAVAKEKNATLMFRLVNPHSTSLIAEGVATKGLGV\r\nHAKSSDWGLQAGYIPVNPNLSKLFGRAPEVIARADNDVNSSLAHGHTAVDLTLSKERLDYLR\r\nQAGLVTGMADGVVASNHAGYEQFEFRVKETSDGRYAVQYRRKGGDDFEAVKVIGNAAGIPLT\r\nADIDMFAIMPHLSNFRDSARSSVTSGDSVTDYLARTRRAASEATGGLDRERIDLLWKIARAG\r\nARSAVGTEARRQFRYDGDMNIGVITDFELEVRNALNRRAHAVGAQDVVQHGTEQNNPFPEAD\r\nEKIFVVSATGESQMLTRGQLKEYIGQQRGEGYVFYENRAYGVAGKSLFDDGLGA",
"organism": "Bordetella pertussis",
"uniprot_code": "P0DKX7",
"uniprot_range_first": 1,
"uniprot_range_last": 364,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MQQSHQAGYANAADRESGIPAAVLDGIKAVAKEKNATLMFRLVNPHSTSLIAEGVATKGL\nGVHAKSSDWGLQAGYIPVNPNLSKLFGRAPEVIARADNDVNSSLAHGHTAVDLTLSKERL\nDYLRQAGLVTGMADGVVASNHAGYEQFEFRVKETSDGRYAVQYRRKGGDDFEAVKVIGNA\nAGIPLTADIDMFAIMPHLSNFRDSARSSVTSGDSVTDYLARTRRAASEATGGLDRERIDL\nLWKIARAGARSAVGTEARRQFRYDGDMNIGVITDFELEVRNALNRRAHAVGAQDVVQHGT\nEQNNPFPEADEKIFVVSATGESQMLTRGQLKEYIGQQRGEGYVFYENRAYGVAGKSLFDD\nGLGAAPGVPSGRSKFSPDVLETVPASPGLRRPSLGAVERQDSGYDSLDGVGSRSFSLGEV\nSDMAAVEAAELEMTRQVLHAGARQDDAEPGVSGASAHWGQRALQGAQAVAAAQRLVHAIA\nLMTQFGRAGSTNTPQEAASLSAAVFGLGEASSAVAETVSGFFRGSSRWAGGFGVAGGAMA\nLGGGIAAAVGAGMSLTDDAPAGQKAAAGAEIALQLTGGTVELASSIALALAAARGVTSGL\nQVAGASAGAAAGALAAALSPMEIYGLVQQSHYADQLDKLAQESSAYGYEGDALLAQLYRD\nKTAAEGAVAGVSAVLSTVGAAVSIAAAASVVGAPVAVVTSLLTGALNGILRGVQQPIIEK\nLANDYARKIDELGGPQAYFEKNLQARHEQLANSDGLRKMLADLQAGWNASSVIGVQTTEI\nSKSALELAAITGNADNLKSVDVFVDRFVQGERVAGQPVVLDVAAGGIDIASRKGERPALT\nFITPLAAPGEEQRRRTKTGKSEFTTFVEIVGKQDRWRIRDGAADTTIDLAKVVSQLVDAN\nGVLKHSIKLDVIGGDGDDVVLANASRIHYDGGAGTNTVSYAALGRQDSITVSADGERFNV\nRKQLNNANVYREGVATQTTAYGKRTENVQYRHVELARVGQLVEVDTLEHVQHIIGGAGND\nSITGNAHDNFLAGGSGDDRLDGGAGNDTLVGGEGQNTVIGGAGDDVFLQDLGVWSNQLDG\nGAGVDTVKYNVHQPSEERLERMGDTGIHADLQKGTVEKWPALNLFSVDHVKNIENLHGSR\nLNDRIAGDDQDNELWGHDGNDTIRGRGGDDILRGGLGLDTLYGEDGNDIFLQDDETVSDD\nIDGGAGLDTVDYSAMIHPGRIVAPHEYGFGIEADLSREWVRKASALGVDYYDNVRNVENV\nIGTSMKDVLIGDAQANTLMGQGGDDTVRGGDGDDLLFGGDGNDMLYGDAGNDTLYGGLGD\nDTLEGGAGNDWFGQTQAREHDVLRGGDGVDTVDYSQTGAHAGIAAGRIGLGILADLGAGR\nVDKLGEAGSSAYDTVSGIENVVGTELADRITGDAQANVLRGAGGADVLAGGEGDDVLLGG\nDGDDQLSGDAGRDRLYGEAGDDWFFQDAANAGNLLDGGDGRDTVDFSGPGRGLDAGAKGV\nFLSLGKGFASLMDEPETSNVLRNIENAVGSARDDVLIGDAGANVLNGLAGNDVLSGGAGD\nDVLLGDEGSDLLSGDAGNDDLFGGQGDDTYLFGVGYGHDTIYESGGGHDTIRINAGADQL\nWFARQGNDLEIRILGTDDALTVHDWYRDADHRVEIIHAANQAVDQAGIEKLVEAMAQYPD\nPGAAAAAPPAARVPDTLMQSLAVNWR",
"mw": 39.38,
"total_mw": 39.38,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Hepes, 150 mM NaCl, 4 mM CaCl2",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.4,
"deuteration": null
},
"purity_method": null,
"name": "Catalytic domain (AC) of B. Pertussis Adenylate Cyclase Toxin (CyaA)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Paris, France",
"full_name": "I2BC-CNRS",
"webpage": "http://www.i2bc.paris-saclay.fr"
}
],
"contributor_name": "Dominique",
"contributor_surname": "DURAND",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2015-06-19",
"storage_temperature": 10.0,
"cell_temperature": 15.0,
"exposure_time": 1.5,
"number_of_frames": 250,
"wavelength": 0.1,
"sample_detector_distance": 1.988,
"concentration_min": null,
"concentration_max": null,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.066,
"s_max": 3.999,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCK9_fit1_model1_img.png",
"software": "AllosMod",
"pdb_link": [
{
"pdb_code": "1yru",
"ext_code": "1YRU",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCK9_fit1_model1.pdb",
"model_mw": 39.37,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 262
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCK9_fit1_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 2.565,
"p_value": 0.0,
"fit_residual_plot": "fit4columns1199_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCK9_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/AC_Model_1YRU00.log",
"software_version": "2.8.3",
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCK9_fit2_model1_img.png",
"software": "AllosMod",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCK9_fit2_model1.pdb",
"model_mw": 39.37,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 262
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCK9_fit2_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.358,
"p_value": 0.00072,
"fit_residual_plot": "fit4columns1200_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCK9_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/AC_Model_AllosModFoxs00.log",
"software_version": "2.8.3",
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "The scattered intensities were displayed on an absolute scale (cm-1) using the scattering of water. Frames were examined individually and 20 identical frames were averaged and further processed. The corresponding concentration was 0.80 g/L.\r\nThree independent determinations of the molecular mass were obtained from the value of I(0)/c, where c is the protein concentration, and using the programs SAXSMow2 and ScÅtter3 available at the URLs http://saxs.ifsc.usp.br/ and https://bl1231.als.lbl.gov/scatter/, respectively. The average value is MWexperimental=40.2 ± 1.0 kDa.\r\n\r\nAC in solution: \r\nTop panel: Adjustment of the curve calculated from the crystal structure of AC extracted from the pdb dataset 1YRU (red curve) after missing loop addition using AllosModFoxs against experimental data (blue dots). chi2=2.57\r\nBottom panel: Adjustment obtained using AllosModFoxs by releasing residues 200-270 comprising helices F through H’ (red curve). Residues 200-270 correspond to the large yellow-light green loop seen in the model displayed on the right. chi2=1.36",
"experiment_description": "Synchrotron SAXS data from solutions of the catalytic domain (AC) of B. Pertussis adenylate cyclase toxin (CyaA) in 20 mM HEPES, 150 mM NaCl, 4 mM CaCl2, pH 7.4 were collected on the SWING beam line at the SOLEIL storage ring (Saint-Aubin, France) using a CCD AVIEX detector at a sample-detector distance of 2.0 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsin θ/λ and 2θ is the scattering angle). 250 successive 1.500 second frames were collected at at 15°C using size-exclusion chromatography SAXS.",
"tags": [],
"intensity_unit": "1/cm",
"experimental_mw": 40.2,
"experimental_mw_error": null,
"guinier_i0_mw": 38.6,
"guinier_i0_mw_error": 2.0,
"porod_mw": 40.1,
"porod_mw_error": null,
"pddf_i0": 0.0252,
"pddf_i0_error": 0.0002,
"guinier_i0": 0.0252,
"guinier_i0_error": 0.0002,
"pddf_rg": 2.62,
"pddf_rg_error": 0.03,
"guinier_rg": 2.59,
"guinier_rg_error": 0.03,
"pddf_dmax": 9.1,
"pddf_dmax_error": 0.5,
"porod_volume": 60.2,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 66,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDCK9_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
