The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
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{
"code": "SASDG37",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "Insights into herpesvirus assembly from the structure of the pUL7:pUL51 complex.",
"publication": {
"title": "Insights into herpesvirus assembly from the structure of the pUL7:pUL51 complex.",
"author_list": "Butt BG, Owen DJ, Jeffries CM, Ivanova L, Hill CH, Houghton JW, Ahmed MF, Antrobus R, Svergun DI, Welch JJ, Crump CM, Graham SC",
"journal": "Elife",
"doi": "10.7554/eLife.53789",
"pmid": "32391791",
"published_date": "2020 May 11"
},
"status": "released",
"submitted_date": "2019-10-17",
"released_date": "2020-05-20"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDG37.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDG37.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG37_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG37_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDG37_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG37_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDG37.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 6M",
"resolution": null
},
"name": "PETRA III",
"city": "DESY; Hamburg",
"country": "Germany",
"beamline_name": "EMBL P12",
"beam_geometry": null,
"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": "Tegument protein UL7",
"short_name": "pUL7",
"sequence": "MAAATADDEGSAATILKQAIAGDRSLVEAAEAISQQTLLRLACEVRQVGDRQPRFTATSIARVDVAPGCRLRFVLDGSPEDAYVTSEDYFKRCCGQSSYRGFAVAVLTANEDHVHSLAVPPLVLLHRFSLFNPRDLLDFELACLLMYLENCPRSHATPSTFAKVLAWLGVAGRRTSPFERVRCLFLRSCHWVLNTLMFMVHVKPFDDEFVLPHWYMARYLLANNPPPVLSALFCATPTSSSFRLPGPPPRSDCVAYNPAGIMGSCWASEEVRAPLVYWWLSETPKRQTSSLFYQFCGSLEVLFQ",
"organism": "Human alphaherpesvirus 1 strain KOS",
"uniprot_code": "A0A110B4Q7",
"uniprot_range_first": 1,
"uniprot_range_last": 296,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MAAATADDEGSAATILKQAIAGDRSLVEAAEAISQQTLLRLACEVRQVGDRQPRFTATSI\nARVDVAPGCRLRFVLDGSPEDAYVTSEDYFKRCCGQSSYRGFAVAVLTANEDHVHSLAVP\nPLVLLHRFSLFNPRDLLDFELACLLMYLENCPRSHATPSTFAKVLAWLGVAGRRTSPFER\nVRCLFLRSCHWVLNTLMFMVHVKPFDDEFVLPHWYMARYLLANNPPPVLSALFCATPTSS\nSFRLPGPPPRSDCVAYNPAGIMGSCWASEEVRAPLVYWWLSETPKRQTSSLFYQFC",
"mw": 33.907,
"total_mw": 33.907,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Tegument protein UL51",
"short_name": "pUL51",
"sequence": "MISGWGARPEEQYEMIRAAVPPSEAEPRLQEALVVVNALLPAPITLDDALGSLDDTRRLVKARALARTYHACMVNLERLARHHPGLEAPTIDGAVAAHQDKMRRLADTCMATILQMYMSVGAADKSADVLVSQAIR",
"organism": "Human alphaherpesvirus 1 strain KOS",
"uniprot_code": "D3YPL0",
"uniprot_range_first": 8,
"uniprot_range_last": 142,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MASLLGAICGWGARPEEQYEMIRAAVPPSEAEPRLQEALVVVNALLPAPITLDDALGSLD\nDTRRLVKARALARTYHACMVNLERLARHHPGLEAPTIDGAVAAHQDKMRRLADTCMATIL\nQMYMSVGAADKSADVLVSQAIRSMAESDVVMEDVAIAERALGLSAFGVAGGTRSGGLGVT\nEAPSLGHPHTPPPEVTLAPAARNGDALPDPKPESCPRVSVPRPTASPTAPRPGPSRAAPC\nVLGQ",
"mw": 14.814,
"total_mw": 29.628,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM tris, 200 mM NaCl, 3% (v/v) glycerol, 0.25 mM TCEP",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "1:2 heterotrimer of pUL7 and pUL51(8-142) from herpes simplex virus 1",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": null,
"full_name": "University of Cambridge",
"webpage": null
}
],
"contributor_name": "Benjamin",
"contributor_surname": "Butt",
"orcid": "https://orcid.org/0000-0001-6718-0470"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2019-05-16",
"storage_temperature": null,
"cell_temperature": 20.2,
"exposure_time": 0.995,
"number_of_frames": 3600,
"wavelength": 0.124,
"sample_detector_distance": 3.0,
"concentration_min": null,
"concentration_max": 4.5,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.079,
"s_max": 7.299,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDG37_fit1_model1_img.png",
"software": "DAMMIN",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "SUPCOMB 23 (r9988)",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDG37_fit1_model1.pdb",
"model_mw": 72.17,
"bead_radius": 2.5,
"log": null,
"symmetry": "P1",
"comment": "Refined DAMMIN model of the HSV-1 pUL7:pUL51(8-142) 1:2 heterotrimer",
"user": 502
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDG37_fit1_fixed_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 1.04,
"p_value": 0.100571,
"fit_residual_plot": "SASDG37_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDG37_fit1.fir",
"fit_log": null,
"software_version": "5.3",
"description": "Fit of the refined DAMMIN model to the HSV-1 pUL7:pUL51 1:2 heterotrimer SAXS profile"
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDG37_fit2_model1_img.png",
"software": "GASBOR",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDG37_fit2_model1.pdb",
"model_mw": null,
"bead_radius": 1.9,
"log": null,
"symmetry": "P1",
"comment": "Representative GASBOR model of the HSV-1 pUL7:pUL51(8-142) 1:2 heterotrimer",
"user": 502
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDG37_fit2_fixed_fit_img.png",
"software": "GASBOR",
"chi_square_value": 1.03,
"p_value": 0.161218,
"fit_residual_plot": "SASDG37_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDG37_fit2.fir",
"fit_log": null,
"software_version": "2.3i",
"description": "Fit of the representative GASBOR model to the HSV-1 pUL7:pUL51(8-142) heterotrimer SAXS profile"
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDG37_fit3_model1_img.png",
"software": "CORAL",
"pdb_link": [
{
"pdb_code": "6t5a",
"ext_code": "6T5A",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDG37_fit3_model1.pdb",
"model_mw": 63.56,
"bead_radius": 1.9,
"log": null,
"symmetry": "P1",
"comment": null,
"user": 502
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDG37_fit3_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.034,
"p_value": 0.1398,
"fit_residual_plot": "SASDG37_fit3_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDG37_fit3.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/coral_100.log",
"software_version": null,
"description": "CRYSOL fit of CORAL model"
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "The quoted experimental molecular mass, that corresponds to a 1:2 pUL7:pUL51(8-142) heterotrimer, was determined from SEC-MALLS-RI measurements performed on identical samples, eluted in parallel to the SEC-SAXS. The SEC-SAXS data for each individual run, Rg correlations through the main elution peak as well as the the SEC-MALLS-RI data and hydrodynamic estimates obtained from QELS are made available in the full-entry zip archive. The CORAL rigid-body refined (atomistic) model displayed in this entry is one example of several alternatives whereby a second copy of pUL51 samples different spatial positions bound within the complex. Additional representations of the 1:2 pUL7:pUL51(8-142) heterotrimeric complex, including those incorporating mass spectrometry cross-linking distance constraints, are also made available in the full entry zip-archive.",
"experiment_description": "Synchrotron SAXS data from the 1:2 heterotrimer of pUL7 and pUL51(8-142) from herpes simplex virus 1 in 20 mM tris, 200 mM NaCl, 3% (v/v) glycerol, 0.25 mM TCEP, pH 7.5 were collected on the EMBL P12 beam line at PETRA III (Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 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 profile displayed represents the average of three individual SEC-SAXS runs. The SEC parameters, per run, were as follows: A 75.00 μl sample at 4.5 mg/ml was injected at a 0.40 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 20°C. Approximately 100 successive 1 second frames were collected through the major SEC-elution peak and processed using CHROMIXS. 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": 67.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 66.99,
"porod_mw_error": null,
"pddf_i0": 3346.0,
"pddf_i0_error": null,
"guinier_i0": 3331.04,
"guinier_i0_error": 2.09,
"pddf_rg": 3.023,
"pddf_rg_error": null,
"guinier_rg": 2.96,
"guinier_rg_error": 0.01,
"pddf_dmax": 11.5,
"pddf_dmax_error": null,
"porod_volume": 115.57,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 9,
"guinier_point_last": 131,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDG37_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:55:24.740692+02:00",
"bragg_peak": []
}
