{ "code": "SASDBY4", "status": "Published", "type_of_curve": "Merged", "angular_unit": "1/nm", "project": { "title": "Dynamic intramolecular regulation of the histone chaperone nucleoplasmin controls histone binding and release.", "publication": { "title": "Dynamic intramolecular regulation of the histone chaperone nucleoplasmin controls histone binding and release.", "author_list": "Warren C, Matsui T, Karp JM, Onikubo T, Cahill S, Brenowitz M, Cowburn D, Girvin M, Shechter D", "journal": "Nat Commun", "doi": "10.1038/s41467-017-02308-3", "pmid": "29263320", "published_date": "2017 Dec 20" }, "status": "released", "submitted_date": "2016-06-02", "released_date": "2017-11-18" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBY4.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBY4.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBY4_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBY4_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBY4_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBY4_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBY4.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Rayonix MX225-HE", "resolution": null }, "name": "Stanford Synchrotron Radiation Lightsource (SSRL)", "city": "Menlo Park, CA", "country": "USA", "beamline_name": "BL4-2", "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": "Nucleoplasmin core + A2", "short_name": "Npm core", "sequence": "ASTASNTSKVEKPVSLIWGCELNEQNKTFAFKIEDEEEKCEHQLALRTVCLGDKAKDEFHIVEIVTQEEGKEKPVPIASLKPSILPMATMVGIELTPPVTFRLKAGSGPVYISGQHVAMEEDYSWAEEEDEGEEEEEEEEDPESP", "organism": "Xenopus laevis", "uniprot_code": "Q6NUC7", "uniprot_range_first": 2, "uniprot_range_last": 145, "oligomerization": "pentamer", "molecular_type": "protein", "uniprot_sequence": null, "mw": 16.165, "total_mw": 80.824, "number_molecules": 5, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "Histone H2A (ΔAla127)", "short_name": "2HA", "sequence": "SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSKSK", "organism": "Xenopus laevis", "uniprot_code": "Q6AZJ8", "uniprot_range_first": 2, "uniprot_range_last": 130, "oligomerization": "pentamer", "molecular_type": "protein", "uniprot_sequence": "MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT\nAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK\nTESSKSAKSK", "mw": 13.879, "total_mw": 69.395, "number_molecules": 5, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "Histone H2B 1.1 (Ser33Thr)", "short_name": "H2B", "sequence": "AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK", "organism": "Xenopus laevis", "uniprot_code": "P02281", "uniprot_range_first": 5, "uniprot_range_last": 126, "oligomerization": "pentamer", "molecular_type": "protein", "uniprot_sequence": "MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAM\nSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT\nKYTSAK", "mw": 13.494, "total_mw": 67.468, "number_molecules": 5, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM Tris. 150 mM NaCl, 1 mM EDTA, 5 mM DTT", "concentration_unit": "mM", "comment": null, "additive": "150mM NaCl, 1mM EDTA, 5mM DTT", "concentration": 20.0, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "Pentameric Nucleoplasmin-histone H2A/H2B complex", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [], "contributor_name": "Michael", "contributor_surname": "Brenowitz", "orcid": null }, { "affiliation": [], "contributor_name": "Sean", "contributor_surname": "Cahill", "orcid": null }, { "affiliation": [], "contributor_name": "Mark", "contributor_surname": "Girvin", "orcid": null }, { "affiliation": [], "contributor_name": "Jerome", "contributor_surname": "Karp", "orcid": null }, { "affiliation": [ { "short_name": "SLAC", "address": "Menlo Park, CA, USA", "full_name": "Stanford Synchrotron Radiation Lightsource", "webpage": "http://www-ssrl.slac.stanford.edu/" } ], "contributor_name": "Tsutomu", "contributor_surname": "Matsui", "orcid": null }, { "affiliation": [], "contributor_name": "Takashi", "contributor_surname": "Onikubo", "orcid": null }, { "affiliation": [], "contributor_name": "David", "contributor_surname": "Shechter", "orcid": null }, { "affiliation": [], "contributor_name": "Christopher", "contributor_surname": "Warren", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2016-01-07", "storage_temperature": 20.0, "cell_temperature": 20.0, "exposure_time": 1.0, "number_of_frames": 55, "wavelength": 0.1127, "sample_detector_distance": 1.7, "concentration_min": null, "concentration_max": null, "sample_volume": null, "flow_rate": null, "s_min": 0.16, "s_max": 2.994, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBY4_fit1_model1_img.png", "software": "DAMFILT", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "r6345", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDBY4_fit1_model1.pdb", "model_mw": 250.736, "bead_radius": 5.75, "log": null, "symmetry": "P5", "comment": "", "user": 131 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBY4_fit2_fit_img.png", "software": null, "chi_square_value": 1.58, "p_value": 0.0, "fit_residual_plot": "SASDBY4_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBY4_fit1.fir", "fit_log": null, "software_version": null, "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBY4_fit2_model1_img.png", "software": "CORAL", "pdb_link": [], "model_title": null, "type_of_model": "mix", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDBY4_fit2_model1.pdb", "model_mw": 223.5, "bead_radius": 1.9, "log": null, "symmetry": "P5", "comment": null, "user": 131 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/Major_site_fit_img.png", "software": "CORAL", "chi_square_value": 1.43, "p_value": 0.0, "fit_residual_plot": "Major_site_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBY4_fit2.fit", "fit_log": null, "software_version": null, "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBY4_fit3_model1_img.png", "software": "CORAL", "pdb_link": [], "model_title": null, "type_of_model": "mix", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDBY4_fit3_model1.pdb", "model_mw": 223.5, "bead_radius": 1.9, "log": null, "symmetry": "P5", "comment": null, "user": 131 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/Minor_site_fit_img.png", "software": "CORAL", "chi_square_value": 1.26, "p_value": 0.000139, "fit_residual_plot": "Minor_site_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBY4_fit3.fit", "fit_log": null, "software_version": null, "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": null, "i0_calibration_standard": null, "description": "The models displayed for this entry are: Top: ab initio bead model representation (derived from individual reconstructions (example fit shown), aligned, spatially averaged and volume-occupancy corrected): Middle: The best CORAL model using the major A2 site (site #1) of A2:H2A/H2B complex as a starting structure (See Figure 5D in the primary citation). Lacking fragments reconstructed by the program CORAL are shown as spheres. Bottom: The best CORAL model using the minor A2 site (site #2) of A2:H2A/H2B complex as a starting structure (See Figure 5D in the primary citation). Lacking fragments reconstructed by the program CORAL are shown as spheres.", "experiment_description": "Synchrotron SAXS data measured from solutions of the pentameric nucleoplasmin-histone H2A/H2B complex in 20 mM Tris 150mM NaCl, 1mM EDTA, 5mM DTT, pH 8.0, were collected on the BL4-2 beam line at the Stanford Synchrotron Radiation Lightsource (Stanford, USA) using a Rayonix MX225-HE detector (I(s) vs s; s = 4π sin θ/λ, where 2θ is the scattering angle and λ=0.1127 nm). Fifty five successive 1 s data frames were collected immediately after the protein complex eluted from a size-exclusion chromatography (SEC) column. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank (derived from the SEC running solvent) was subtracted and the individual solvent-corrected SAXS profiles were scaled and averaged to produce the final merged SAXS data profile.", "tags": [], "intensity_unit": null, "experimental_mw": 251.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": 251.0, "pddf_i0": 2822.0, "pddf_i0_error": 8.0, "guinier_i0": 2875.52, "guinier_i0_error": 14.75, "pddf_rg": 4.32, "pddf_rg_error": 0.01, "guinier_rg": 4.39, "guinier_rg_error": 0.03, "pddf_dmax": 14.0, "pddf_dmax_error": null, "porod_volume": 402.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 16, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDBY4_datloglog_img.png", "symmetry": null, "last_modified": "2021-08-18T17:28:04.360641+02:00", "bragg_peak": [] }