{ "code": "SASDFC4", "status": "Published", "type_of_curve": "Extrapolated to infinite dilution", "angular_unit": "1/nm", "project": { "title": "Solution structure and flexibility of the condensin HEAT-repeat subunit Ycg1.", "publication": { "title": "Solution structure and flexibility of the condensin HEAT-repeat subunit Ycg1.", "author_list": "Manalastas-Cantos K, Kschonsak M, Haering CH, Svergun DI", "journal": "J Biol Chem", "doi": "10.1074/jbc.RA119.008661", "pmid": "31350339", "published_date": "2019 Sep 13" }, "status": "released", "submitted_date": "2019-03-20", "released_date": "2019-07-26" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFC4.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFC4.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFC4_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFC4_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFC4_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFC4_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFC4.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": "Condensin complex subunit 3-like protein", "short_name": "Ycg1", "sequence": ">tr|G0SHK2|G0SHK2_CHATD Condensin complex subunit 3-like protein OS=Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) 24-1006\r\nPDNALRTQVTTVFREAQRTTASHRKLVVTLRKIQEACCYEPATGQKQSGAAAALSEFDED\r\nDFNTEFVRCALRILPVKKSEGVGEKTVRFVSLFLRHAIEKDNELLGDTQMDEDDADNSTM\r\nPETPSTRLTSHLMETILPMLMAKDKFVRYRAAQLLAHIVNSLDAIDDDLYQKLRAGLLRR\r\nIHDKEPMVRAQAVLGLGRLAGNALDEEPGAGDSDLDGDDDGPGGASGVSLMDKLMDVMKN\r\nDPSADVRRTLLVNLPITPKTLPSLLERARDQDPATRRAVYSRLLPALGDFRHLSLSMREK\r\nLLRWGLRDRDENVRKAAARLFRERWIEDCAGTPRPEPGQPIELSPPNMDALLELLERIDV\r\nVNSGGENGIALEAMRGFWEGRPDYRDAMVFDDHFFETLSAESVFALRTFNDFCRNEAGGK\r\nYEALIEEKLPEVTKLAFYLERYIKVLIDAIKRAEEQGEEEEEDTAEQEFIVEQLLHIALT\r\nLDYADEVGRRKMFALLRQTLSIPELPEECTKLTVMVLRDLCAPDAAGEKEFTSVVLEAVA\r\nDVHDTIVDEDDDDANVPAEDDESFVSARSEVSRESTPAPGGGEGGGSNSRKRGRSPTPKM\r\nTEEEAAAKAIREIMINMKCLHIVQCMLQNVQGQLQSNDNLISMLNNLVVPAVRSHEAPVR\r\nERGLVCLGLCALLDRSLAEENLTLFIHFFAKGHTALQITALHILTDILVVHGAQLLSANP\r\nTLLKVYVKALRSGAKHPELQAVAVVAASKLLLGRVVSDRDVAAELLKTLVVAYFEPASAG\r\nNQSVRQALNYFLPVFCYSRAENQDLMRRVALDALHTLYNVREGFDDDDADIDDEMVSLAT\r\nIGACLVDWTDPRKVYTPDAGGLQAEKHVNADVHLDFAKAILERLEGNVPREEKKVLASLL\r\nSKLYISPASSPDKTRETYRVVSAAVDTNLLPDTTSRNALYKIHVSLGKIVNALDGAVPSV\r\nETASVAGSTGTGIGTTTTAATGR", "organism": "Chaetomium thermophilum", "uniprot_code": "G0SHK2", "uniprot_range_first": 24, "uniprot_range_last": 1006, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MPPRTRSTRSSRSSSAIDIPEETPDNALRTQVTTVFREAQRTTASHRKLVVTLRKIQEAC\nCYEPATGQKQSGAAAALSEFDEDDFNTEFVRCALRILPVKKSEGVGEKTVRFVSLFLRHA\nIEKDNELLGDTQMDEDDADNSTMPETPSTRLTSHLMETILPMLMAKDKFVRYRAAQLLAH\nIVNSLDAIDDDLYQKLRAGLLRRIHDKEPMVRAQAVLGLGRLAGNALDEEPGAGDSDLDG\nDDDGPGGASGVSLMDKLMDVMKNDPSADVRRTLLVNLPITPKTLPSLLERARDQDPATRR\nAVYSRLLPALGDFRHLSLSMREKLLRWGLRDRDENVRKAAARLFRERWIEDCAGTPRPEP\nGQPIELSPPNMDALLELLERIDVVNSGGENGIALEAMRGFWEGRPDYRDAMVFDDHFFET\nLSAESVFALRTFNDFCRNEAGGKYEALIEEKLPEVTKLAFYLERYIKVLIDAIKRAEEQG\nEEEEEDTAEQEFIVEQLLHIALTLDYADEVGRRKMFALLRQTLSIPELPEECTKLTVMVL\nRDLCAPDAAGEKEFTSVVLEAVADVHDTIVDEDDDDANVPAEDDESFVSARSEVSRESTP\nAPGGGEGGGSNSRKRGRSPTPKMTEEEAAAKAIREIMINMKCLHIVQCMLQNVQGQLQSN\nDNLISMLNNLVVPAVRSHEAPVRERGLVCLGLCALLDRSLAEENLTLFIHFFAKGHTALQ\nITALHILTDILVVHGAQLLSANPTLLKVYVKALRSGAKHPELQAVAVVAASKLLLGRVVS\nDRDVAAELLKTLVVAYFEPASAGNQSVRQALNYFLPVFCYSRAENQDLMRRVALDALHTL\nYNVREGFDDDDADIDDEMVSLATIGACLVDWTDPRKVYTPDAGGLQAEKHVNADVHLDFA\nKAILERLEGNVPREEKKVLASLLSKLYISPASSPDKTRETYRVVSAAVDTNLLPDTTSRN\nALYKIHVSLGKIVNALDGAVPSVETASVAGSTGTGIGTTTTAATGRRVTRGSVSAGSGTG\nAGRRSISRASSVSTNADRPASASAAVPGSKAASTIEEEEEKEQEEEEEEEEKEEKEEEEE\nEEEEENVDEETQLAMQLQADTTAAQSREGSVQIKREEDDSESEASDATVVRGSVGTGRRV\nKQEEDDDF", "mw": 108.325, "total_mw": 108.325, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "25 mM Tris, 300 mM NaCl, 1mM DTT", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "Condensin complex subunit 3-like protein, Ycg1, extrapolated to infinite dilution", "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": "Karen", "contributor_surname": "Manalastas-Cantos", "orcid": "" } ], "concentration_method": null, "concentration_unit": null, "date": "2016-10-20", "storage_temperature": 13.0, "cell_temperature": 10.0, "exposure_time": 0.05, "number_of_frames": 20, "wavelength": 0.124, "sample_detector_distance": 4.0, "concentration_min": 0.25, "concentration_max": 0.5, "sample_volume": null, "flow_rate": null, "s_min": 0.051, "s_max": 2.5, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFC4_fit1_model1_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "2.8.3", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDFC4_fit1_model1.pdb", "model_mw": 101.0, "bead_radius": 1.8, "log": null, "symmetry": "P1", "comment": null, "user": 425 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/ycg1-free-7_UkhwoIz_fixed_fit_img.png", "software": "DAMMIF", "chi_square_value": 0.735, "p_value": 0.962851, "fit_residual_plot": "ycg1-free-7_UkhwoIz_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFC4_fit1.fir", "fit_log": null, "software_version": "2.8.3", "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFC4_fit2_model1_img.png", "software": "SREFLEX", "pdb_link": [ { "pdb_code": "5oqq", "ext_code": "5OQQ", "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/SASDFC4_fit2_model1.pdb", "model_mw": 94.36, "bead_radius": null, "log": "https://www.sasbdb.org/media/log_files/log_F1cJpYw.txt", "symmetry": "P1", "comment": null, "user": 425 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/rc04_4JnoF6I_fixed_fit_img.png", "software": "SREFLEX", "chi_square_value": 0.827, "p_value": 0.002218, "fit_residual_plot": "rc04_4JnoF6I_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFC4_fit2.fit", "fit_log": null, "software_version": "2.8.3", "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "2.8.3", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of Ycg1, extrapolated to infinite dilution, in 25 mM Tris 300 mM NaCl 1mM DTT, pH 7.5 were collected on the EMBL P12 beam line at PETRA III (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 4 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.3 and 0.5 mg/ml were measured at 10°C. 20 successive 0.050 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The low angle data collected at lower concentrations were extrapolated to infinite dilution and merged with the higher concentration data to yield the final composite scattering curve.", "tags": [], "intensity_unit": null, "experimental_mw": 109.0, "experimental_mw_error": null, "guinier_i0_mw": 102.0, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 7915.0, "pddf_i0_error": null, "guinier_i0": 7926.0, "guinier_i0_error": 108.0, "pddf_rg": 4.618, "pddf_rg_error": null, "guinier_rg": 4.6, "guinier_rg_error": 0.1, "pddf_dmax": 15.63, "pddf_dmax_error": null, "porod_volume": 236.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 11, "guinier_point_last": 108, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDFC4_datloglog_img.png", "symmetry": null, "last_modified": "2023-06-21T07:56:39.492710+02:00", "bragg_peak": [] }