{ "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": [] }