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": "SASDCL9",
"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/SASDCL9.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCL9.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCL9_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCL9_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCL9_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCL9_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCL9.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
},
{
"long_name": "Calmodulin",
"short_name": "CaM",
"sequence": "MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNG\r\nTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDE\r\nMIREADIDGDGQVNYEEFVQMMTAK",
"organism": "Homo sapiens",
"uniprot_code": "P62158",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": null,
"mw": 16.837,
"total_mw": 16.837,
"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) in complex with calmodulin",
"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": 1.987,
"concentration_min": null,
"concentration_max": null,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.061,
"s_max": 4.004,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCL9_fit1_model1_img.png",
"software": "BUNCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "08",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCL9_fit1_model1.pdb",
"model_mw": 56.3,
"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/SASDCL9_fit1_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.956,
"p_value": 0.0,
"fit_residual_plot": "fit4columns1207_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCL9_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/ACCAM_Bunch00.log",
"software_version": "2.8.3",
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCL9_fit2_model1_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "2.1",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCL9_fit2_model1.pdb",
"model_mw": 563.0,
"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/SASDCL9_fit2_fit_img.png",
"software": "EOM/GAJOE",
"chi_square_value": 1.41,
"p_value": 0.000713,
"fit_residual_plot": "fit4columns1209_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCL9_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/logFile_Ensemble_VmzgjMW.log",
"software_version": "2.1",
"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 0.82 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 The average value is MWexperimental=56.3 kDa.\r\nAC-CAM complex: \r\nTop panel: Comparison of the experimental data (blue dots) with the calculated scattering pattern (red line) of the BUNCH model shown on the right. chi2=1.96. Each CaM domain were handled as rigid bodies while the program searches an optimal conformation of the inter-domain helix of CaM.\r\nBottom panel: Typical ensemble of conformations describing the AC:CaM complex, obtained using the program EOM and displayed after superimposition of the AC moiety of each conformation. chi2=1.41. The corresponding scattering curve is shown in red superimposed over experimental data (blue dots).",
"experiment_description": "Synchrotron SAXS data from solutions of the catalytic domain (AC) of B. Pertussis adenylate cyclase toxin (CyaA) in complex with calmodulin 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": 56.3,
"experimental_mw_error": null,
"guinier_i0_mw": 56.3,
"guinier_i0_mw_error": 3.0,
"porod_mw": 51.9,
"porod_mw_error": null,
"pddf_i0": 0.0383,
"pddf_i0_error": 0.0003,
"guinier_i0": 0.0383,
"guinier_i0_error": 0.0003,
"pddf_rg": 2.97,
"pddf_rg_error": 0.03,
"guinier_rg": 2.92,
"guinier_rg_error": 0.03,
"pddf_dmax": 9.8,
"pddf_dmax_error": 0.5,
"porod_volume": 77.9,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 58,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDCL9_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
