{ "code": "SASDFM3", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/A", "project": { "title": "Histone chaperone exploits intrinsic disorder to switch acetylation specificity.", "publication": { "title": "Histone chaperone exploits intrinsic disorder to switch acetylation specificity.", "author_list": "Danilenko N, Lercher L, Kirkpatrick J, Gabel F, Codutti L, Carlomagno T", "journal": "Nat Commun", "doi": "10.1038/s41467-019-11410-7", "pmid": "31387991", "published_date": "2019 Aug 6" }, "status": "released", "submitted_date": "2019-02-27", "released_date": "2019-07-10" }, "pddf_data": null, "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFM3.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFM3_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFM3_kratky_img.png", "pddf_plot": null, "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFM3_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFM3.sascif", "experiment": { "instrument": { "detector": { "type": "SANS", "name": "6Li-Scintillator 1 mm thickness + photomultiplier", "resolution": 5.3 }, "name": "FRM2", "city": "Munich", "country": "Germany", "beamline_name": "KWS1", "beam_geometry": null, "type_of_source": "neutron source", "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": "Vacuolar protein sorting-associated protein 75 (1-225 aa)", "short_name": "Vps75 1-225", "sequence": "MMSDQENENEHAKAFLGLAKCEEEVDAIEREVELYRLNKMKPVYEKRDAYIDEIAEFWKI\r\nVLSQHVSFANYIRASDFKYIDTIDKIKVEWLALESEMYDTRDFSITFHFHGIEGDFKEQQ\r\nVTKVFQIKKGKDDQEDGILTSEPVPIEWPQSYDSINPDLIKDKRSPEGKKKYRQGMKTIF\r\nGWFRWTGLKPGKEFPHGDSLASLFSEEIYPFCVKYYAEAQRDLED", "organism": "Saccharomyces cerevisiae", "uniprot_code": "P53853", "uniprot_range_first": 1, "uniprot_range_last": 225, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MMSDQENENEHAKAFLGLAKCEEEVDAIEREVELYRLNKMKPVYEKRDAYIDEIAEFWKI\nVLSQHVSFANYIRASDFKYIDTIDKIKVEWLALESEMYDTRDFSITFHFHGIEGDFKEQQ\nVTKVFQIKKGKDDQEDGILTSEPVPIEWPQSYDSINPDLIKDKRSPEGKKKYRQGMKTIF\nGWFRWTGLKPGKEFPHGDSLASLFSEEIYPFCVKYYAEAQRDLEDEEGESGLSADGDSED\nDDGSLGEVDLPLSDEEPSSKKRKV", "mw": 26.554, "total_mw": 53.108, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "Histone acetyltransferase RTT109", "short_name": "Rtt109", "sequence": "MSLNDFLSSVLPVSEQFEYLSLQSIPLETHAVVTPNKDDKRVPKSTIKTQHFFSLFHQGK\r\nVFFSLEVYVYVTLWDEADAERLIFVSKADTNGYCNTRVSVRDITKIILEFILSIDPNYYL\r\nQKVKPAIRSYKKISPELISAASTPARTLRILARRLKQSGSTVLKEIESPRFQQDLYLSFT\r\nCPREILTKICLFTRPASQYLFPDSSKNSKKHILNGEELMKWWGFILDRLLIECFQNDTQA\r\nKLRIPGEDPARVRSYLRGMKYPLWQVGDIFTSKENSLAVYNIPLFPDDPKARFIHQLAEE\r\nDRLLKVSLSSFWIELQERQEFKLSVTSSVMGISGYSLATPSLFPSSADVIVPKSRKQFRA\r\nIKKYITGEEYDTEEGAIEAFTNIRDFLLLRMATNLQSLTGKREHRERNQPVPASNINTLA\r\nITMLKPRKKAKALPKT", "organism": "Saccharomyces cerevisiae", "uniprot_code": "Q07794", "uniprot_range_first": 1, "uniprot_range_last": 436, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MSLNDFLSSVLPVSEQFEYLSLQSIPLETHAVVTPNKDDKRVPKSTIKTQHFFSLFHQGK\nVFFSLEVYVYVTLWDEADAERLIFVSKADTNGYCNTRVSVRDITKIILEFILSIDPNYYL\nQKVKPAIRSYKKISPELISAASTPARTLRILARRLKQSGSTVLKEIESPRFQQDLYLSFT\nCPREILTKICLFTRPASQYLFPDSSKNSKKHILNGEELMKWWGFILDRLLIECFQNDTQA\nKLRIPGEDPARVRSYLRGMKYPLWQVGDIFTSKENSLAVYNIPLFPDDPKARFIHQLAEE\nDRLLKVSLSSFWIELQERQEFKLSVTSSVMGISGYSLATPSLFPSSADVIVPKSRKQFRA\nIKKYITGEEYDTEEGAIEAFTNIRDFLLLRMATNLQSLTGKREHRERNQPVPASNINTLA\nITMLKPRKKAKALPKT", "mw": 50.095, "total_mw": 50.095, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "Histone chaperone ASF1", "short_name": "Asf1", "sequence": "MSIVSLLGIKVLNNPAKFTDPYEFEITFECLESLKHDLEWKLTYVGSSRSLDHDQELDSI\r\nLVGPVPVGVNKFVFSADPPSAELIPASELVSVTVILLSCSYDGREFVRVGYYVNNEYDEE\r\nELRENPPAKVQVDHIVRNILAEKPRVTRFNIVWDNENEGDLYPPEQPGV", "organism": null, "uniprot_code": "P32447", "uniprot_range_first": 1, "uniprot_range_last": 169, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MSIVSLLGIKVLNNPAKFTDPYEFEITFECLESLKHDLEWKLTYVGSSRSLDHDQELDSI\nLVGPVPVGVNKFVFSADPPSAELIPASELVSVTVILLSCSYDGREFVRVGYYVNNEYDEE\nELRENPPAKVQVDHIVRNILAEKPRVTRFNIVWDNENEGDLYPPEQPGVDDEEEEDDEEE\nDDDEDDEDDEDDDQEDGEGEAEEAAEEEEEEEEKTEDNETNLEEEEEDIENSDGDEEEGE\nEEVGSVDKNEDGNDKKRRKIEGGSTDIESTPKDAARSTN", "mw": 19.125, "total_mw": 19.125, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "Histone H3.2 (35-135 aa)", "short_name": "H3 (35-135)", "sequence": "VKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAY \r\nLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA", "organism": "Xenopus laevis", "uniprot_code": "P84233", "uniprot_range_first": 35, "uniprot_range_last": 135, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE\nLLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI\nMPKDIQLARRIRGERA", "mw": 11.747, "total_mw": 11.747, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "Histone H4", "short_name": "H4", "sequence": "MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK\r\nVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG", "organism": "Xenopus laevis", "uniprot_code": "P62799", "uniprot_range_first": 1, "uniprot_range_last": 103, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK\nVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG", "mw": 11.367, "total_mw": 11.367, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50 mM citrate, 150 mM NaCl, 5 mM BME, 100% D2O", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 6.5, "deuteration": null }, "purity_method": null, "name": "Complex with 1H histone chaperone Asf1 and histones H3 and H4, 2H histone acetyltransferase Rtt109 and histone chaperone Vps75 (1H Asf1-H3:H4, 2H Rtt109-Vps75) acquired in 100% v/v D2O", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Germany", "full_name": "Leibniz University of Hannover", "webpage": "https://www.uni-hannover.de" } ], "contributor_name": "Nataliya", "contributor_surname": "Danilenko", "orcid": "https://orcid.org/0000-0003-4885-5051" } ], "concentration_method": null, "concentration_unit": null, "date": "2017-03-04", "storage_temperature": 25.0, "cell_temperature": 25.0, "exposure_time": 21600.0, "number_of_frames": null, "wavelength": 0.5, "sample_detector_distance": 4.0, "concentration_min": 3.85, "concentration_max": 3.85, "sample_volume": null, "flow_rate": null, "s_min": 0.127, "s_max": 3.455, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFM3_fit1_model1_img.png", "software": "HADDOCK", "pdb_link": [ { "pdb_code": "6o22", "ext_code": "6O22", "ext_type": "pdb", "difference_with_model": "derived" } ], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDFM3_fit1_model1.pdb", "model_mw": 144.0, "bead_radius": null, "log": "https://www.sasbdb.org/media/log_files/new190718_12003.log", "symmetry": null, "comment": null, "user": 420 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/new190718_12003_fit_img.png", "software": "CRYSON", "chi_square_value": 15.132, "p_value": 0.0, "fit_residual_plot": null, "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFM3_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/new190718_12003.log", "software_version": null, "description": "" } ], "estimated_volume_method": null, "pddf_software": null, "pddf_software_version": null, "i0_calibration_standard": null, "description": null, "experiment_description": "SANS data from solutions of the Asf1-H3:H4-Rtt109-Vps75 protein complex (protonated Asf1-H3:H4 bound to perdeuterated Rtt109-Vps75) in 50 mM citrate, 150 mM NaCl, 5 mM BME, 100% D2O, pD 6.5 were collected on the KWS1 instrument at FRM2 (Munich, Germany) using a SANS 6Li-Scintillator 1 mm thickness + photomultiplier detector. Due to a combination of negative (from 1H Asf1-H3:H4) and positive (from perdeuterated Rtt109-Vps75) contrasts the Rg obtained from the Guinier approximation is negative. The data were recorded at two detector configurations: 1) 4 m for 6 hrs using a neutron wavelength of 0.5 nm and; 2) 1.5 m for 2.5 hrs using a neutron wavelength of 0.5 nm. Both measurement were performed on the same sample at 3.85 mg/mL, measured at 25°C.", "tags": [], "intensity_unit": null, "experimental_mw": 145.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": null, "pddf_i0_error": null, "guinier_i0": 0.017, "guinier_i0_error": 0.0063, "pddf_rg": null, "pddf_rg_error": null, "guinier_rg": -2.81, "guinier_rg_error": 0.327, "pddf_dmax": null, "pddf_dmax_error": null, "porod_volume": null, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 3, "guinier_point_last": 10, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDFM3_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }