{ "code": "SASDB48", "status": "Published", "type_of_curve": "Other", "angular_unit": "1/A", "project": { "title": "The herpes viral transcription factor ICP4 forms a novel DNA recognition complex.", "publication": { "title": "The herpes viral transcription factor ICP4 forms a novel DNA recognition complex.", "author_list": "Tunnicliffe RB, Lockhart-Cairns MP, Levy C, Mould AP, Jowitt TA, Sito H, Baldock C, Sandri-Goldin RM, Golovanov AP", "journal": "Nucleic Acids Res", "doi": "10.1093/nar/gkx419", "pmid": "28505309", "published_date": "2017 Jul 27" }, "status": "released", "submitted_date": "2016-11-28", "released_date": "2017-05-30" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDB48.dat", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDB48.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB48_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB48_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDB48_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB48_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDB48.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 2M", "resolution": null }, "name": "Diamond Light Source", "city": "Didcot", "country": "UK", "beamline_name": "B21", "beam_geometry": "1 x 5 mm", "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": "Major viral transcription factor ICP4", "short_name": "ICP4N", "sequence": "PAASAGRIERRRARAAVAGRDATGRFTAGQPRRVELDADATSG\r\nAFYARYRDGYVSGEPWPGAGPPPPGRVLYGGLGDSRPGLWGAPEAEEARRRFEASGAPAA\r\nVWAPELGDAAQQYALITRLLYTPDAEAMGWLQNPRVVPGDVALDQACFRISGAARNSSSF\r\nITGSVARAVPHLGYAMAAGRFGWGLAHAAAAVAMSRRYDRAQKGFLLTSLRRAYAPLLAR\r\nENAALTG", "organism": "Human alphaherpesvirus 1", "uniprot_code": "P08392", "uniprot_range_first": 258, "uniprot_range_last": 487, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MASENKQRPGSPGPTDGPPPTPSPDRDERGALGWGAETEEGGDDPDHDPDHPHDLDDARR\nDGRAPAAGTDAGEDAGDAVSPRQLALLASMVEEAVRTIPTPDPAASPPRTPAFRADDDDG\nDEYDDAADAAGDRAPARGREREAPLRGAYPDPTDRLSPRPPAQPPRRRRHGRWRPSASST\nSSDSGSSSSSSASSSSSSSDEDEDDDGNDAADHAREARAVGRGPSSAAPAAPGRTPPPPG\nPPPLSEAAPKPRAAARTPAASAGRIERRRARAAVAGRDATGRFTAGQPRRVELDADATSG\nAFYARYRDGYVSGEPWPGAGPPPPGRVLYGGLGDSRPGLWGAPEAEEARRRFEASGAPAA\nVWAPELGDAAQQYALITRLLYTPDAEAMGWLQNPRVVPGDVALDQACFRISGAARNSSSF\nITGSVARAVPHLGYAMAAGRFGWGLAHAAAAVAMSRRYDRAQKGFLLTSLRRAYAPLLAR\nENAALTGAAGSPGAGADDEGVAAVAAAAPGERAVPAGYGAAGILAALGRLSAAPASPAGG\nDDPDAARHADADDDAGRRAQAGRVAVECLAACRGILEALAEGFDGDLAAVPGLAGARPAS\nPPRPEGPAGPASPPPPHADAPRLRAWLRELRFVRDALVLMRLRGDLRVAGGSEAAVAAVR\nAVSLVAGALGPALPRDPRLPSSAAAAAADLLFDNQSLRPLLAAAASAPDAADALAAAAAS\nAAPREGRKRKSPGPARPPGGGGPRPPKTKKSGADAPGSDARAPLPAPAPPSTPPGPEPAP\nAQPAAPRAAAAQARPRPVAVSRRPAEGPDPLGGWRRQPPGPSHTAAPAAAALEAYCSPRA\nVAELTDHPLFPVPWRPALMFDPRALASIAARCAGPAPAAQAACGGGDDDDNPHPHGAAGG\nRLFGPLRASGPLRRMAAWMRQIPDPEDVRVVVLYSPLPGEDLAGGGASGGPPEWSAERGG\nLSCLLAALANRLCGPDTAAWAGNWTGAPDVSALGAQGVLLLSTRDLAFAGAVEFLGLLAS\nAGDRRLIVVNTVRACDWPADGPAVSRQHAYLACELLPAVQCAVRWPAARDLRRTVLASGR\nVFGPGVFARVEAAHARLYPDAPPLRLCRGGNVRYRVRTRFGPDTPVPMSPREYRRAVLPA\nLDGRAAASGTTDAMAPGAPDFCEEEAHSHAACARWGLGAPLRPVYVALGREAVRAGPARW\nRGPRRDFCARALLEPDDDAPPLVLRGDDDGPGALPPAPPGIRWASATGRSGTVLAAAGAV\nEVLGAEAGLATPPRREVVDWEGAWDEDDGGAFEGDGVL", "mw": 24.31, "total_mw": 48.62, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "Immediate Early 3", "short_name": "IE3", "sequence": "CCGATCGTCCACACGGAGC", "organism": null, "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "dimer", "molecular_type": "DNA", "uniprot_sequence": null, "mw": 5.839, "total_mw": 11.678, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM HEPES, 150 mM NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.4, "deuteration": null }, "purity_method": null, "name": "Major viral transcription factor ICP4/Immediate Early 3 DNA (ICP4N IE3_19mer) complex", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Manchester, UK", "full_name": "University of Manchester", "webpage": "http://www.manchester.ac.uk/" } ], "contributor_name": "Michael", "contributor_surname": "Lockhart", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2015-07-27", "storage_temperature": 20.0, "cell_temperature": 20.0, "exposure_time": 1.0, "number_of_frames": null, "wavelength": 0.1, "sample_detector_distance": 3.9, "concentration_min": null, "concentration_max": null, "sample_volume": null, "flow_rate": null, "s_min": 0.367, "s_max": 2.513, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/ICP4N_refine_407_edit_cdgh_W0AmBsY_img.png", "software": "PHENIX", "pdb_link": [ { "pdb_code": "5mhk", "ext_code": "5MHK", "ext_type": "pdb", "difference_with_model": "identical" } ], "model_title": null, "type_of_model": "atomic", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDB48_fit1_model1.pdb", "model_mw": 53.44, "bead_radius": 1.9, "log": null, "symmetry": "P1", "comment": "", "user": 23 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDB48_fit1_fitfoxs_img.png", "software": "FoXS", "chi_square_value": 2.4, "p_value": 0.0, "fit_residual_plot": "SASDB48_fit1_fitfoxsresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDB48_fit1.dat", "fit_log": null, "software_version": null, "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDB48_fit2_model1_img.png", "software": "DAMFILT", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "5.0", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDB48_fit2_model1.pdb", "model_mw": null, "bead_radius": 2.5, "log": "https://www.sasbdb.org/media/log_files/run_1_pjjFw0m.log", "symmetry": "", "comment": "17 models were run in slow mode", "user": 23 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDB48_fit2_fit_img.png", "software": "DAMMIF", "chi_square_value": 1.34, "p_value": 0.163, "fit_residual_plot": "SASDB48_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDB48_fit2.fir", "fit_log": null, "software_version": "", "description": null } ], "estimated_volume_method": null, "pddf_software": "ScÅtter", "pddf_software_version": "ScÅtter 3.0g", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of Major viral transcription factor ICP4/Immediate Early 3 DNA (ICP4N IE3_19mer) complex in 20 mM HEPES, 150 mM NaCl, pH 7.4 were collected using HPLC SEC-SAXS at the B21 beam line at the Diamond Light Source (Oxfordshire, UK) using a Pilatus 2M detector at a sample-detector distance of 3.9 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4π sin θ/λ and 2θ is the scattering angle). The sample was separated using a Shodex KW-403 SEC column and Agilent HPLC before exposure to X-rays to isolate the ICP4N IE3_19mer complex from any dissociated monomer. 50 µL of ICP4N•IE3_19mer complex was loaded onto the Shodex column and the eluent was flowed through the SAXS beam at 0.15 mL/min; the buffer used as the background was collected after one SEC column volume. Data were collected at 20°C at one second intervals.", "tags": [], "intensity_unit": null, "experimental_mw": 60.4, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 109.6, "pddf_i0_error": null, "guinier_i0": 114.0, "guinier_i0_error": 0.44, "pddf_rg": 2.51, "pddf_rg_error": null, "guinier_rg": 2.54, "guinier_rg_error": 0.019, "pddf_dmax": 8.3, "pddf_dmax_error": null, "porod_volume": 89.71, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 32, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDB48_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }