{ "code": "SASDG44", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/A", "project": { "title": "Intermediate-resolution crystal structure of the human adenovirus B serotype 3 fibre knob in complex with the EC2-EC3 fragment of desmoglein 2.", "publication": { "title": "Intermediate-resolution crystal structure of the human adenovirus B serotype 3 fibre knob in complex with the EC2-EC3 fragment of desmoglein 2.", "author_list": "Vassal-Stermann E, Hutin S, Fender P, Burmeister WP", "journal": "Acta Crystallogr F Struct Biol Commun", "doi": "10.1107/S2053230X19015784", "pmid": "31797817", "published_date": "2019 Dec 1" }, "status": "released", "submitted_date": "2019-08-13", "released_date": "2019-12-03" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDG44.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDG44.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG44_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG44_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDG44_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG44_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDG44.sascif", "experiment": { "instrument": { "detector": { "type": "Dectris", "name": "Pilatus 1M", "resolution": 172.0 }, "name": "ESRF", "city": "Grenoble", "country": "France", "beamline_name": "BM29", "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": "Human adenovirus serotype 3 fibre knob", "short_name": "HAd3K", "sequence": "HHHHHHSQDPANSIALKNNTLWTGPKPEANCIIEYGKQNPDSKLTLILVKNGGIVNGYVTLMGASDYVNTLFKNKNVSINVELYFDATGHILPDSSSLKTDLELKYKQTADFSARGFMPSTTAYPFVLPNAGTHNENYIFGQCYYKASDGALFPLEVTVMLNKRLPDSRTSYVMTFLWSLNAGLAPETTQATLITSPFTFSYIREDD", "organism": "Human adenovirus serotype 3", "uniprot_code": "P04501", "uniprot_range_first": 130, "uniprot_range_last": 318, "oligomerization": "trimer", "molecular_type": "protein", "uniprot_sequence": "MAKRARLSTSFNPVYPYEDESSSQHPFINPGFISPDGFTQSPNGVLSLKCVNPLTTASGS\nLQLKVGSGLTVDTTDGSLEENIKVNTPLTKSNHSINLPIGNGLQIEQNKLCSKLGNGLTF\nDSSNSIALKNNTLWTGPKPEANCIIEYGKQNPDSKLTLILVKNGGIVNGYVTLMGASDYV\nNTLFKNKNVSINVELYFDATGHILPDSSSLKTDLELKYKQTADFSARGFMPSTTAYPFVL\nPNAGTHNENYIFGQCYYKASDGALFPLEVTVMLNKRLPDSRTSYVMTFLWSLNAGLAPET\nTQATLITSPFTFSYIREDD", "mw": 23.072, "total_mw": 69.216, "number_molecules": 3, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "Human desmoglein 2 extracellular domain 2 and 3", "short_name": "EC2-EC3", "sequence": "QGAMEVLDINDNEPVFTQDVFVGSVEELSAAHTLVMKINATDADEPNTLNSKISYRIVSLEPAYPPVFYLNKDTGEIYTTSVTLDREEHSSYTLTVEARDGNGEVTDKPVKQAQVQIRILDVNDNIPVVENKVLEGMVEENQVNVEVTRIKVFDADEIGSDNWLANFTFASGNEGGYFHIETDAQTNEGIVTLIKEVDYEEMKNLDFSVIVANKAAFHKSIRSKYKPTPIPIKVKVKNVKEGI", "organism": "Homo sapiens", "uniprot_code": "Q14126", "uniprot_range_first": 157, "uniprot_range_last": 380, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MARSPGRAYALLLLLICFNVGSGLHLQVLSTRNENKLLPKHPHLVRQKRAWITAPVALRE\nGEDLSKKNPIAKIHSDLAEERGLKITYKYTGKGITEPPFGIFVFNKDTGELNVTSILDRE\nETPFFLLTGYALDARGNNVEKPLELRIKVLDINDNEPVFTQDVFVGSVEELSAAHTLVMK\nINATDADEPNTLNSKISYRIVSLEPAYPPVFYLNKDTGEIYTTSVTLDREEHSSYTLTVE\nARDGNGEVTDKPVKQAQVQIRILDVNDNIPVVENKVLEGMVEENQVNVEVTRIKVFDADE\nIGSDNWLANFTFASGNEGGYFHIETDAQTNEGIVTLIKEVDYEEMKNLDFSVIVANKAAF\nHKSIRSKYKPTPIPIKVKVKNVKEGIHFKSSVISIYVSESMDRSSKGQIIGNFQAFDEDT\nGLPAHARYVKLEDRDNWISVDSVTSEIKLAKLPDFESRYVQNGTYTVKIVAISEDYPRKT\nITGTVLINVEDINDNCPTLIEPVQTICHDAEYVNVTAEDLDGHPNSGPFSFSVIDKPPGM\nAEKWKIARQESTSVLLQQSEKKLGRSEIQFLISDNQGFSCPEKQVLTLTVCECLHGSGCR\nEAQHDSYVGLGPAAIALMILAFLLLLLVPLLLLMCHCGKGAKGFTPIPGTIEMLHPWNNE\nGAPPEDKVVPSFLPVDQGGSLVGRNGVGGMAKEATMKGSSSASIVKGQHEMSEMDGRWEE\nHRSLLSGRATQFTGATGAIMTTETTKTARATGASRDMAGAQAAAVALNEEFLRNYFTDKA\nASYTEEDENHTAKDCLLVYSQEETESLNASIGCCSFIEGELDDRFLDDLGLKFKTLAEVC\nLGQKIDINKEIEQRQKPATETSMNTASHSLCEQTMVNSENTYSSGSSFPVPKSLQEANAE\nKVTQEIVTERSVSSRQAQKVATPLPDPMASRNVIATETSYVTGSTMPPTTVILGPSQPQS\nLIVTERVYAPASTLVDQPYANEGTVVVTERVIQPHGGGSNPLEGTQHLQDVPYVMVRERE\nSFLAPSSGVQPTLAMPNIAVGQNVTVTERVLAPASTLQSSYQIPTENSMTARNTTVSGAG\nVPGPLPDFGLEESGHSNSTITTSSTRVTKHSTVQHSYS", "mw": 27.339, "total_mw": 54.678, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM Tris-HCl, 150 mM NaCl, 3 mM CaCl2", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "Adenovirus Ad3 fibre knob in complex with the EC2-EC3 fragment of desmoglein 2", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "IBS", "address": "Grenoble, France", "full_name": "Institut de Biologie Structurale", "webpage": "" } ], "contributor_name": "Wim", "contributor_surname": "Burmeister", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2017-01-26", "storage_temperature": 293.0, "cell_temperature": 293.0, "exposure_time": 1.0, "number_of_frames": 2000, "wavelength": 0.099, "sample_detector_distance": 2.864, "concentration_min": null, "concentration_max": 2.4, "sample_volume": 100.0, "flow_rate": 0.1, "s_min": 0.141, "s_max": 2.005, "total_exposure_time": null, "seccolumn": 14 }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDG44_fit1_model1_img.png", "software": "Other", "pdb_link": [ { "pdb_code": "6sit", "ext_code": "6SIT", "ext_type": "pdb", "difference_with_model": "identical" } ], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDG44_fit1_model1.pdb", "model_mw": 90.53, "bead_radius": null, "log": null, "symmetry": "3-fold", "comment": "3:1 complex built from asymmetric unit structure. HAd3K has 3-fold symmetry, EC2-EC3 has not.", "user": 226 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDG44_fit1_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 0.795, "p_value": 0.0, "fit_residual_plot": "SASDG44_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDG44_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/complex3-100.log", "software_version": "7.1", "description": "3:1 complex present in 40 % of the particles" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDG44_fit2_model1_img.png", "software": "Other", "pdb_link": [ { "pdb_code": "6sit", "ext_code": "6SIT", "ext_type": "pdb", "difference_with_model": "identical" } ], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDG44_fit2_model1.pdb", "model_mw": 117.3, "bead_radius": null, "log": null, "symmetry": "3-fold", "comment": "3:2 complex built from asymmetric unit structure. HAd3K has 3-fold symmetry, EC2-EC3 has not.", "user": 226 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDG44_fit2_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 0.514, "p_value": 0.0, "fit_residual_plot": "SASDG44_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDG44_fit2.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/complex3-200.log", "software_version": "7.1", "description": "Fit with the £:2 complex structure, present in 40 % of the particles." }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDG44_fit3_model1_img.png", "software": "Other", "pdb_link": [ { "pdb_code": "6sit", "ext_code": "6SIT", "ext_type": "pdb", "difference_with_model": "identical" } ], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDG44_fit3_model1.pdb", "model_mw": 90.53, "bead_radius": null, "log": null, "symmetry": "3-fold", "comment": "3:1 complex built from asymmetric unit structure. HAd3K has 3-fold symmetry, EC2-EC3 has not.", "user": 226 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDG44_fit3_model2_img.png", "software": "Other", "pdb_link": [ { "pdb_code": "6sit", "ext_code": "6SIT", "ext_type": "pdb", "difference_with_model": "identical" } ], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDG44_fit3_model2.pdb", "model_mw": 117.3, "bead_radius": null, "log": null, "symmetry": "3-fold", "comment": "3:1 complex built from asymmetric unit structure. HAd3K has 3-fold symmetry, EC2-EC3 has not.", "user": 226 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDG44_fit3_fixed_fit_img.png", "software": "OLIGOMER", "chi_square_value": 0.4, "p_value": 1e-06, "fit_residual_plot": "SASDG44_fit3_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDG44_fit3.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/oligomer_MG0kL7h.log", "software_version": "7.1", "description": "Combination of 40 % 3:1 and 60 % 3:2 complexes (by number)." } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": "Three different stoichiometries are possible for the Had3K: human desmoglein 2 EC2-EC3 complex : 3:1, 3:2 and 3:3. The SAXS experiment is used in order to determine the possible stoichiometries in solution.", "experiment_description": "Synchrotron SAXS data from solutions of adenovirus Ad3 fibre knob in complex with the EC2-EC3 fragment of desmoglein 2 in 20 mM Tris-HCl, 150 mM NaCl, 3 mM CaCl2, pH 8 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.099 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 100.00 μl sample at 2.4 mg/ml was injected at a 0.10 ml/min flow rate onto a GE Superdex 200 Increase 3.2/300 column at 293°C. 2000 successive 1 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.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 119.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 114.0, "porod_mw_error": null, "pddf_i0": 258.3, "pddf_i0_error": null, "guinier_i0": 255.03, "guinier_i0_error": 0.61, "pddf_rg": 3.5, "pddf_rg_error": null, "guinier_rg": 3.42, "guinier_rg_error": 0.1, "pddf_dmax": 11.17, "pddf_dmax_error": null, "porod_volume": 188.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 12, "guinier_point_last": 35, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDG44_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }