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{
"code": "SASDFM7",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/A",
"project": {
"title": "Histone chaperone exploits intrinsic disorder to switch acetylation specificity (Asf1-H3:H4-Rtt109-Vps75 protein complex, data for docking block selections)",
"publication": {
"title": "Histone chaperone exploits intrinsic disorder to switch acetylation specificity (Asf1-H3:H4-Rtt109-Vps75 protein complex, data for docking block selections)",
"author_list": "Danilenko N, Lercher L, Kirkpatrick J, Gabel F, Codutti L, Carlomagno T",
"journal": "Nat Commun",
"doi": null,
"pmid": null,
"published_date": "2019 Aug 6"
},
"status": "released",
"submitted_date": "2019-06-17",
"released_date": "2019-07-10"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFM7.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFM7.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFM7_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFM7_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFM7_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFM7_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFM7.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "128 linear sensitive multidetector",
"name": "Reuter-Stokes 3He",
"resolution": 0.8
},
"name": "Institut Laue-Langevin (ILL)",
"city": "Grenoble",
"country": "France",
"beamline_name": "D22",
"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 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
},
{
"long_name": "Histone H3 full-length",
"short_name": "H3 FL",
"sequence": "MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALR \r\nEIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAY \r\nLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA",
"organism": "Xenopus laevis",
"uniprot_code": "Q6PI79",
"uniprot_range_first": 1,
"uniprot_range_last": 136,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTE\nLLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTI\nMPKDIQLARRIRGERA",
"mw": 15.328,
"total_mw": 15.328,
"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, 42% 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, histones H3 and H4, acetylatransferase Rtt109, 2H histone chaperone Vps75 (1-225aa) in 42% 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": "2016-11-14",
"storage_temperature": null,
"cell_temperature": 25.1,
"exposure_time": 3600.0,
"number_of_frames": 1,
"wavelength": 0.6,
"sample_detector_distance": 4.0,
"concentration_min": null,
"concentration_max": 4.9,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.122,
"s_max": 2.405,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFM7_fit1_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "3q66",
"ext_code": "3Q66",
"ext_type": "pdb",
"difference_with_model": "identical"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDFM7_fit1_model1.pdb",
"model_mw": 103.0,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 420
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDFM7_fit1_fixed_fit_img.png",
"software": "CRYSON",
"chi_square_value": 0.286,
"p_value": 0.184911,
"fit_residual_plot": "fit4columns2422_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFM7_fit1.fit",
"fit_log": null,
"software_version": null,
"description": "Fit to the original X-ray structure (PDB 3q66)"
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFM7_fit2_model1_img.png",
"software": "GROMACS",
"pdb_link": [
{
"pdb_code": "3q66",
"ext_code": "3Q66",
"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/SASDFM7_fit2_model1.pdb",
"model_mw": 101.1,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 420
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDFM7_fit2_fixed_fit_img.png",
"software": "CRYSON",
"chi_square_value": 0.244,
"p_value": 0.184911,
"fit_residual_plot": "fit4columns2423_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFM7_fit2.fit",
"fit_log": null,
"software_version": null,
"description": "Fit ot the selected MD model based on PDB 3q66."
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "4.6",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "SANS data from solutions the Asf1-H3:H4-Rtt109-Vps75 protein complex (1H Asf1-H3:H4-Rtt109, bound to 2H-labelled Vps75(1-225)) in 50 mM citrate, 150 mM NaCl, 5 mM BME, 100% D2O, pD 6.5 were collected on the D22 instrument at the ILL (Grenoble, France) using a 3He multidetector 128 linear sensitive Reuter-Stokes detector detector at a sample-detector/Collimation distance of 4 m/4 m and at a wavelength of λ = 0.6 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 4.9 mg/ml was measured at 25°C for 1 h.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 149.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
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"pddf_i0": 0.1471,
"pddf_i0_error": null,
"guinier_i0": 0.14658,
"guinier_i0_error": 0.0014,
"pddf_rg": 2.78,
"pddf_rg_error": null,
"guinier_rg": 2.741,
"guinier_rg_error": 0.04,
"pddf_dmax": 9.0,
"pddf_dmax_error": null,
"porod_volume": null,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 17,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDFM7_datloglog_img.png",
"symmetry": null,
"last_modified": "2022-08-15T14:51:04.900446+02:00",
"bragg_peak": []
}
