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{
"code": "SASDFT8",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Structural basis for DNA recognition and allosteric control of the retinoic acid receptors RAR–RXR",
"publication": {
"title": "Structural basis for DNA recognition and allosteric control of the retinoic acid receptors RAR–RXR",
"author_list": "Osz J, McEwen A, Bourguet M, Przybilla F, Peluso-Iltis C, Poussin-Courmontagne P, Mély Y, Cianférani S, Jeffries C, Svergun D, Rochel N",
"journal": "Nucleic Acids Research",
"doi": "10.1093/nar/gkaa697",
"pmid": null,
"published_date": "2020 Aug 25"
},
"status": "released",
"submitted_date": "2020-06-24",
"released_date": "2020-08-11"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFT8.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFT8.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFT8_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFT8_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFT8_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFT8_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFT8.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 2M",
"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": "Retinoic acid receptor alpha, RAR",
"short_name": "mRARa",
"sequence": "MGSSHHHHHHSSGLVPRGSHMIYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFDVGMSKESVRNDRNKKKKEAPKPECSESYTLTPEVGELIEKVRKAHQETFPALCQLGKYTTNNSSEQRVSLDIDLWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVFAFANQLLPLEMDDAETGLLSAICLICGDRQDLEQPDKVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVITLKMEIPGSMPPLIQEMLENSEGLD",
"organism": "Mus musculus",
"uniprot_code": "P11416",
"uniprot_range_first": 84,
"uniprot_range_last": 421,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MASNSSSCPTPGGGHLNGYPVPPYAFFFPPMLGGLSPPGALTSLQHQLPVSGYSTPSPAT\nIETQSSSSEEIVPSPPSPPPLPRIYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNM\nVYTCHRDKNCIINKVTRNRCQYCRLQKCFDVGMSKESVRNDRNKKKKEAPKPECSESYTL\nTPEVGELIEKVRKAHQETFPALCQLGKYTTNNSSEQRVSLDIDLWDKFSELSTKCIIKTV\nEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNA\nGFGPLTDLVFAFANQLLPLEMDDAETGLLSAICLICGDRQDLEQPDKVDMLQEPLLEALK\nVYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVITLKMEIPGSMPPLIQEMLENSEGL\nDTLSGQSGGGTRDGGGLAPPPGSCSPSLSPSSHRSSPATQSP",
"mw": 40.786,
"total_mw": 40.786,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Retinoic acid receptor RXR-alpha",
"short_name": "mRXRa",
"sequence": "FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDRNENEVESTSSANEDMPVEKILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAPHQAT",
"organism": "Mus musculus",
"uniprot_code": "P28700",
"uniprot_range_first": 135,
"uniprot_range_last": 467,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MDTKHFLPLDFSTQVNSSSLNSPTGRGSMAVPSLHPSLGPGIGSPLGSPGQLHSPISTLS\nSPINGMGPPFSVISSPMGPHSMSVPTTPTLGFGTGSPQLNSPMNPVSSTEDIKPPLGLNG\nVLKVPAHPSGNMASFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNK\nDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDRNENEVESTSSANEDMPVEKI\nLEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLD\nDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVS\nKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRF\nAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAPHQAT",
"mw": 37.745,
"total_mw": 37.745,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "DNA response element HoxB13 DR0",
"short_name": "HoxB13 DR0",
"sequence": "GAAGGTCAAGGCCAAG\r\nCTTCCAGTTCCGGTTC",
"organism": null,
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "DNA",
"uniprot_sequence": null,
"mw": 9.905,
"total_mw": 9.905,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Tris, pH 8, 150 mM NaCl, 5% v/v glycerol, 1 mM CHAPS, 4 mM MgSO4, 1 mM TCEP",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 8.0,
"deuteration": null
},
"purity_method": null,
"name": "The retinoic acid receptor (RAR-RXR heterodimer) bound to the DNA response element HoxB13 DR0",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "EMBL-Hamburg",
"address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
"full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
"webpage": "http://www.embl-hamburg.de/index.php"
}
],
"contributor_name": "Cy M",
"contributor_surname": "Jeffries",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2014-01-19",
"storage_temperature": 20.0,
"cell_temperature": 10.0,
"exposure_time": 1.0,
"number_of_frames": 45,
"wavelength": 0.124,
"sample_detector_distance": 3.0,
"concentration_min": null,
"concentration_max": 5.5,
"sample_volume": 100.0,
"flow_rate": 0.5,
"s_min": 0.02,
"s_max": 4.512,
"total_exposure_time": null,
"seccolumn": 1
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFT8_fit1_model1_img.png",
"software": "CORAL",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "5",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDFT8_fit1_model1.pdb",
"model_mw": 87.02,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/crysol_summary_FqDsEYb.txt",
"symmetry": "P1",
"comment": null,
"user": 9
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDFT8_fit1_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.25,
"p_value": 0.0332,
"fit_residual_plot": "SASDFT8_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFT8_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/RARRXRHoxb13Csaxs00.log",
"software_version": null,
"description": "CRYSOL fit of a CORAL model repersentative"
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "4.6",
"i0_calibration_standard": null,
"description": "SEC-SAXS analysis was performed in parallel with right-angle laser light scattering (RALLS) and refractive index measurements at room temperature. The Rg-correlation through the SEC-SAXS peak, as well as the results from coupled RALLS/RI, and alternative CORAL rigid-body refined models that fit the scattering data are included in the full entry zip archive. The quoted experimental molecular weight was determined from RALLS/RI measurements that were recorded from the same sample eluting from the column using a split-flow SEC-SAXS-light scattering configuration as described in Graewert et al., (2015) Sci. Reports. 5, 10734: doi: 10.1038/srep10734. The MW estimated directly from the SAXS data using Bayesian inference is ca. 86 kDa in the interval 81-93 kDa (Hajizadeh et al., (2018) Sci. Reports. 8(1):7204. doi: 10.1038/s41598-018-25355-2).",
"experiment_description": "Synchrotron SAXS data from solutions of the retinoic acid receptor (RXR/RAR heterodimer) bound to the DNA response element HoxB13 DR0 in 20 mM Tris, pH 8, 150 mM NaCl, 5% v/v glycerol, 1 mM CHAPS, 4 mM MgSO4, 1 mM TCEP were collected on the EMBL P12 beam line at PETRA III (Hamburg, Germany) using a Pilatus 2M 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 SEC parameters were as follows: A 100.00 μl sample at 5.5 mg/ml was injected at a 0.50 ml/min flow rate onto a GE Superdex 200 10/300 column at 20°C. 45 successive 1 second frames were collected through the SEC-elution sample peak. 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": 103.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 83.0,
"porod_mw_error": null,
"pddf_i0": 82.07,
"pddf_i0_error": null,
"guinier_i0": 80.97,
"guinier_i0_error": 0.22,
"pddf_rg": 3.96,
"pddf_rg_error": null,
"guinier_rg": 3.78,
"guinier_rg_error": 0.05,
"pddf_dmax": 14.5,
"pddf_dmax_error": null,
"porod_volume": 132.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 22,
"guinier_point_last": 124,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDFT8_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}
