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{
"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": []
}
