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{
"code": "SASDEH3",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Cooperative DNA Binding of the Plasmid Partitioning Protein TubR from the Bacillus cereus pXO1 Plasmid.",
"publication": {
"title": "Cooperative DNA Binding of the Plasmid Partitioning Protein TubR from the Bacillus cereus pXO1 Plasmid.",
"author_list": "Hayashi I, Oda T, Sato M, Fuchigami S",
"journal": "J Mol Biol",
"doi": "10.1016/j.jmb.2018.11.001",
"pmid": "30414406",
"published_date": "2018 Nov 7"
},
"status": "released",
"submitted_date": "2018-08-23",
"released_date": "2018-11-13"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEH3.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEH3.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEH3_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEH3_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEH3_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEH3_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEH3.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus3 2M",
"resolution": 0.172
},
"name": "Photon Factory (PF), High Energy Accelerator Research Organization (KEK)",
"city": "Tsukuba",
"country": "Japan",
"beamline_name": "BL-10C",
"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": "S48 DNA strand 1",
"short_name": null,
"sequence": "ATCATACTTCGGAAATATATACCGAAGTATTTACGGCTTTTATAACGGTATTAAATTCCGTATAATGAT",
"organism": null,
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "DNA",
"uniprot_sequence": null,
"mw": 21.324,
"total_mw": 21.324,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "S48 DNA strand 2",
"short_name": null,
"sequence": "ATCATACTTCGGAAATATATACCGAAGTATTTACGGCTTTTATAACGGTATTAAATTCCGTATAATGAT",
"organism": null,
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "DNA",
"uniprot_sequence": null,
"mw": 21.324,
"total_mw": 21.324,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "TubR of the pXO1-like plasmid pBc10987 from B. cereus (Bc-TubR)",
"short_name": "Bc-TubR",
"sequence": "GSHMSNISMSSSEIIDVLCENLNDGIWALRVLYAEGAMNKEKLWDYINQYHKDYQIENEKDYEGKKILPSRYALDIMTARLEGAGLISFKAIGRVRIYDVTDLGNVLIKELEKRVEKNN",
"organism": null,
"uniprot_code": "B7JTH0",
"uniprot_range_first": 1,
"uniprot_range_last": 116,
"oligomerization": "decamer",
"molecular_type": "protein",
"uniprot_sequence": "MSNISMSSSEIIDVLCENLNDGIWALRVLYAEGAMNKEKLWDYINQYHKDYQIENEKDYE\nGKKILPSRYALDIMTARLEGAGLISFKAIGRVRIYDVTDLGNVLIKELEKRVEKNN",
"mw": 13.685,
"total_mw": 136.85,
"number_molecules": 10,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "0.1 M NaCl, 10 mM Tris",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 8.0,
"deuteration": null
},
"purity_method": null,
"name": "TubR protein of the pXO1-like plasmid pBc10987 from B. cereus (Bc-TubR) bound to S48 DNA (Bc-TubR : S48 DNA complex)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Japan",
"full_name": "Yokohama City University",
"webpage": "https://www.yokohama-cu.ac.jp"
}
],
"contributor_name": "Takashi",
"contributor_surname": "Oda",
"orcid": ""
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-11-28",
"storage_temperature": 8.0,
"cell_temperature": 8.0,
"exposure_time": 20.0,
"number_of_frames": 1,
"wavelength": 0.15,
"sample_detector_distance": 2.012,
"concentration_min": null,
"concentration_max": null,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.079,
"s_max": 2.781,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEH3_fit1_model1_img.png",
"software": "Molecular Dynamics Frame",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEH3_fit1_model1.pdb",
"model_mw": 174.8,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 360
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEH3_fit1_model2_img.png",
"software": "Molecular Dynamics Frame",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEH3_fit1_model2.pdb",
"model_mw": 148.1,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 360
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/Frction_0_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 0.8963,
"p_value": 0.0,
"fit_residual_plot": "Frction_0_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEH3_fit1.fit",
"fit_log": null,
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEH3_fit2_model1_img.png",
"software": "DAMFILT",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "DAMFILT 5.",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEH3_fit2_model1.pdb",
"model_mw": null,
"bead_radius": 4.5,
"log": null,
"symmetry": null,
"comment": null,
"user": 360
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/11_BcR-S48_Scale-sub_55-69_abs-1_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 0.907,
"p_value": 0.0,
"fit_residual_plot": "11_BcR-S48_Scale-sub_55-69_abs-1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEH3_fit2.fir",
"fit_log": null,
"software_version": null,
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "The molecular weight (MW) of the Bc-TubR : S48 DNA complex was estimated from the macromolecular volume using the method of Fischer et al. (J. Appl. Crystallogr. 43, 101–109, 2010; SAXMow program). However, the MW estimate is likely not an accurate value because the sample is a complex of protein and DNA. The theoretical SAXS curve of the molecular dynamics model was calculated as the mixture of the two models (one model contains four TubR dimers plus DNA, another model contains five TubR dimers plus DNA). For the mixed model, the fractions of each are 0.4 and 0.6, respectively. A low resolution dummy atom model was built by DAMMIF. Ten independently built models were generated, spatially aligned and then bead-occupancy and volume corrected using DAMAVER to generate an averaged spatial representation of the complex (damfilt). The the fit to the SAXS data from an individual dummy atom model from the cohort of models used to obtain the average representation is shown, specifically that with the smallest chi-square value.\r\nSample concentration: UNKNOWN",
"experiment_description": "Synchrotron SAXS data from a solution of the Bc-TubR:S48 DNA complex in 0.1 M NaCl, 10 mM Tris, pH 8 were collected on the BL-10C beam line at the Photon Factory (PF), High Energy Accelerator Research Organization (KEK) storage ring (Tsukuba, Japan) using a Pilatus3 2M detector at a sample-detector distance of 2.0 m and at a wavelength of λ = 0.15 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Data were collected for a 20 s X-ray exposure time at a sample temperature of 8°C. 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": "1/cm",
"experimental_mw": 249.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 0.08148,
"pddf_i0_error": null,
"guinier_i0": 0.07952,
"guinier_i0_error": 0.0003,
"pddf_rg": 6.57,
"pddf_rg_error": null,
"guinier_rg": 6.11,
"guinier_rg_error": 0.04,
"pddf_dmax": 23.0,
"pddf_dmax_error": null,
"porod_volume": 305.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 39,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDEH3_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
