{ "code": "SASDFT3", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/A", "project": { "title": "A Dissection of Oligomerisation by the TRIM28 Tripartite Motif and the Interaction with Members of the Krab-ZFP Family.", "publication": { "title": "A Dissection of Oligomerisation by the TRIM28 Tripartite Motif and the Interaction with Members of the Krab-ZFP Family.", "author_list": "Sun Y, Keown JR, Black MM, Raclot C, Demarais N, Trono D, Turelli P, Goldstone DC", "journal": "J Mol Biol", "doi": "10.1016/j.jmb.2019.05.002", "pmid": "31078555", "published_date": "2019 May 9" }, "status": "released", "submitted_date": "2019-03-06", "released_date": "2019-05-16" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFT3.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFT3.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFT3_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFT3_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFT3_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFT3_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFT3.sascif", "experiment": { "instrument": { "detector": { "type": "Dectris", "name": "Pilatus 1M", "resolution": 172.0 }, "name": "Australian Synchrotron", "city": "Melbourne", "country": "Australia", "beamline_name": "SAXS/WAXS", "beam_geometry": "Point", "type_of_source": "X-ray synchrotron", "point_source": true, "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": "Transcription intermediary factor 1-beta", "short_name": "TRIM28", "sequence": "GPGEAQELLEHCGVCRERLRPERDPRLLPCLHSACSACLGPATPAAANNSGDGGSAGDGAMVDCPVCKQQCYSKDIVENYFMRDSGSKASSDSQDANQCCTSCEDNAPATSYCVECSEPLCETCVEAHQRVKYTKDHTVRSTGPAKTRDGERTVYCNVHKHEPLVLFCESCDTLTCRDCQLNAHKDHQYQFLEDAVRNQRKLLASLVKRLGDKHATLQKNTKEVRSSIRQVSDVQKRVQVDVKMAILQIMKELNKRGRVLVNDAQKVTEGQQERLERQHWTMTKIQKHQEHILRFASWALESDNNTALLLSKKLIYFQLHRALKMIVDPVEPHGEMKFQWDLNAWTKSAEAFGKIVAERPGTNS", "organism": "Mus musculus", "uniprot_code": "Q62318", "uniprot_range_first": 58, "uniprot_range_last": 418, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MAASAAATAAASAATAASAASGSPGSGEGSAGGEKRPAASSAAAASAAASSPAGGGGEAQ\nELLEHCGVCRERLRPERDPRLLPCLHSACSACLGPATPAAANNSGDGGSAGDGAMVDCPV\nCKQQCYSKDIVENYFMRDSGSKASSDSQDANQCCTSCEDNAPATSYCVECSEPLCETCVE\nAHQRVKYTKDHTVRSTGPAKTRDGERTVYCNVHKHEPLVLFCESCDTLTCRDCQLNAHKD\nHQYQFLEDAVRNQRKLLASLVKRLGDKHATLQKNTKEVRSSIRQVSDVQKRVQVDVKMAI\nLQIMKELNKRGRVLVNDAQKVTEGQQERLERQHWTMTKIQKHQEHILRFASWALESDNNT\nALLLSKKLIYFQLHRALKMIVDPVEPHGEMKFQWDLNAWTKSAEAFGKIVAERPGTNSTG\nPGPMAPPRAPGPLSKQGSGSSQPMEVQEGYGFGSDDPYSSAEPHVSGMKRSRSGEGEVSG\nLLRKVPRVSLERLDLDLTSDSQPPVFKVFPGSTTEDYNLIVIERGAAAAAAGQAGTVPPG\nAPGAPPLPGMAIVKEEETEAAIGAPPAAPEGPETKPVLMPLTEGPGAEGPRLASPSGSTS\nSGLEVVAPEVTSAPVSGPGILDDSATICRVCQKPGDLVMCNQCEFCFHLDCHLPALQDVP\nGEEWSCSLCHVLPDLKEEDGSLSLDGADSTGVVAKLSPANQRKCERVLLALFCHEPCRPL\nHQLATDSTFSMEQPGGTLDLTLIRARLQEKLSPPYSSPQEFAQDVGRMFKQFNKLTEDKA\nDVQSIIGLQRFFETRMNDAFGDTKFSAVLVEPPPLNLPSAGLSSQELSGPGDGP", "mw": 40.928, "total_mw": 81.856, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "Zinc finger protein 809 N-terminal MBP fusion", "short_name": "MBP-ZFP809", "sequence": "MLVIWINGDKGYNGLAQVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTNGSTSGGGGSNNNPPTPTPSSGSGHHHHHHSAALEVLFQGPGMGLVSFEDVAVDFTLEEWQDLDAAQRTLYRDVMLETYSSLVFLDPCIAKPKLIFNLERGFGPWSLAEASSRSLP", "organism": "Mus musculus", "uniprot_code": "G3X9G7", "uniprot_range_first": 1, "uniprot_range_last": 74, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MGLVSFEDVAVDFTLEEWQDLDAAQRTLYRDVMLETYSSLVFLDPCIAKPKLIFNLERGF\nGPWSLAEASSRSLPGVHNVSTLSDTSKKIPKTRLRQLRKTNQKTPSEDTIEAELKARQEV\nSKGTTSRHRRAPVKSLCRKSQRTKNQTSYNDGNLYECKDCEKVFCNNSTLIKHYRRTHNV\nYKPYECDECSKMYYWKSDLTSHQKTHRQRKRIYECSECGKAFFRKSHLNAHERTHSGEKP\nYECTECRKAFYYKSDLTRHKKTHLGEKPFKCEECKKAFSRKSKLAIHQKKHTGEKPYECT\nECKKAFSHQSQLTAHRIAHSSENPYECKECNKSFHWKCQLTAHQKRHTGVTYFQEVVFQQ\nITVSDWTGNLSENGPHRPTWTWAYGIMDFVKAWSRCIIGGGL", "mw": 52.099, "total_mw": 52.099, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "10 mM Tris 300 mM NaCl 0.1 mM TCEP", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "Murine transcription intermediary factor 1-beta, TRIM28 RBCC assembly-null mutation R184D, complexed with the Krab domain of ZFP809 fused to an N-terminal MBP", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Auckland, New Zealand", "full_name": "The University of Auckland", "webpage": "https://www.auckland.ac.nz" } ], "contributor_name": "Yunyuan", "contributor_surname": "Sun", "orcid": "" } ], "concentration_method": null, "concentration_unit": null, "date": "2017-08-10", "storage_temperature": null, "cell_temperature": 16.0, "exposure_time": 1.0, "number_of_frames": 48, "wavelength": 0.113, "sample_detector_distance": 3.3, "concentration_min": 0.15, "concentration_max": 0.3, "sample_volume": null, "flow_rate": null, "s_min": 0.043, "s_max": 2.843, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFT3_fit1_model1_img.png", "software": "GASBOR", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDFT3_fit1_model1.pdb", "model_mw": null, "bead_radius": 1.9, "log": "https://www.sasbdb.org/media/log_files/complex.log", "symmetry": "p1", "comment": null, "user": 423 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/complex_fit_img.png", "software": "GASBOR", "chi_square_value": 0.69, "p_value": 0.099471, "fit_residual_plot": "complex_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFT3_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/complex.log", "software_version": "2.3i", "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of TRIM28 RBCC_R184D in complex with MBP-Krab ZFP809 in 10 mM Tris 300 mM NaCl 0.1 mM TCEP, pH 8 were collected using size-exclusion chromatography SAXS (SEC-SAXS) on the SAXS/WAXS beam line at the Australian Synchrotron (Melbourne, Australia) using a Pilatus 1M detector at a sample-detector distance of 3.3 m and at a wavelength of λ = 0.113 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). SEC-SAXS was performed at 16 °C using the GE-Healthcare S200 5/150 analytical SEC column at a flow rate of 0.5 mL/min. Two successive 50 μL samples were loaded at 1:1 RBCC to MBP-Krab and 1:1.5 RBCC to MBP-Krab molar ratios, at concentrations of 11.2 and 14.3 mg/mL, respectively. The data were collected through the SEC peaks of each individual run as a series of 48 x 1 second exposures . The data were normalized to the intensity of the transmitted beam and radially averaged and the the scattering of an appropriate solvent-blank was subtracted. Both samples yielded identical scattering curves after buffer subtraction and therefore have been scaled and merged to generate the final SAXS profile displayed in this entry.", "tags": [], "intensity_unit": "1/cm", "experimental_mw": 138.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 0.06258, "pddf_i0_error": null, "guinier_i0": 0.062, "guinier_i0_error": 0.00024, "pddf_rg": 6.58, "pddf_rg_error": null, "guinier_rg": 6.38, "guinier_rg_error": 0.046, "pddf_dmax": 22.0, "pddf_dmax_error": null, "porod_volume": 252.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 3, "guinier_point_last": 43, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDFT3_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }