{ "code": "SASDFD4", "status": "Published", "type_of_curve": "Merged", "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/SASDFD4.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFD4.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFD4_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFD4_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFD4_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFD4_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFD4.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 }, { "long_name": "Condensin complex subunit 2", "short_name": "Brn1", "sequence": ">tr|G0SBJ6|G0SBJ6_CHATD Condensin complex subunit 2 OS=Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) 515-634\r\nKIHEDILSYFDQALQKNWTSAEHWRIRKIKDVNKPNEPTRQRKEKQPFEIDFVSPLDKAL\r\nAEIIYTKASSNATISMPKKDWKSKTKNLLPDDKHFSSKQLLSLFLKPKARMGRRRVLKTS", "organism": "Chaetomium thermophilum", "uniprot_code": "G0SBJ6", "uniprot_range_first": 515, "uniprot_range_last": 634, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MPRVAPHRRSGSRVGSGSFLESPFKSPAKLPLADDAIEKAERAQGRKAAHEAQINQIRSA\nATSTPRKSSGAFNPDLDHGASPNSTPRTPHRRRSAVRETILLDDEEVVVGGRAVTPMKRV\nPILANFEEWMKMATDNKINAANSWNFALIDYFHDMSLLKEGDSVNFQKASCTLDGCVKIY\nTSRVDSVATETGKLLSGLADSRDSKKKDREDGGEDDDEEEEEVDEDGTVRKKPKKKTQRS\nSEATLAPSFASLQLKKLELEFAVDPFFKKASADFDEGGAKGLLLNHLMIDSQGRIVFDSS\nDDAEDVAEASAKPSREADDERPDSEDADADGDISMTDRDASAPGQVETQPEEEDEDVEID\nVAALGAKYFPDLSILDSLDVCPSLKTFDLGDPSGSLYIPFLKVPDDWRHDQEKEKTPGLG\nSLGNKSAMFIDDENPDGFDDDDGLGTFDMGADVGFGEGGEAWAKEAALEPHAMRVYDAGL\nGDGTEGDGEGDGADLMDAGTGEYVVAMSQPRSAEKIHEDILSYFDQALQKNWTSAEHWRI\nRKIKDVNKPNEPTRQRKEKQPFEIDFVSPLDKALAEIIYTKASSNATISMPKKDWKSKTK\nNLLPDDKHFSSKQLLSLFLKPKARMGRRRVLKTSRIGNIDSERHDDLPEGEVDEAFWATQ\nKAPLANGNDRPGRHPDDDDEPLPQGDYDANFFADDGLPFAGGMDDDDDMDRFSDAREHFS\nPEPGAGGPGMNSTAGLQDLATGIMGQNPGDGAFGTNLVTQGRRVRPEYVQYARVAKKVDV\nRRLKEEIWKGMGFDELTSSNSNDTSQLQTPARQAEEQRSPESADGPNGKDKDPTLRFTDV\nMNSLQRVYPKQVMDDISTSYCFICLLHLANEKGLVIEKTDTLDELYIRKDWSAVVGDE", "mw": 17.0, "total_mw": 17.0, "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, bound to condensin complex subunit 2, Brn1 (Ycg1-Brn1)", "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": 0.5, "concentration_max": 5.0, "sample_volume": null, "flow_rate": null, "s_min": 0.047, "s_max": 2.511, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFD4_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/SASDFD4_fit1_model1.pdb", "model_mw": 153.0, "bead_radius": 1.7, "log": null, "symmetry": "P1", "comment": null, "user": 425 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/ycg1-kle-5_su5qzO1_fixed_fit_img.png", "software": "DAMMIF", "chi_square_value": 0.684, "p_value": 0.003314, "fit_residual_plot": "ycg1-kle-5_su5qzO1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFD4_fit1.fir", "fit_log": null, "software_version": "2.8.3", "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFD4_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/SASDFD4_fit2_model1.pdb", "model_mw": 106.0, "bead_radius": null, "log": "https://www.sasbdb.org/media/log_files/log_TC1Jeri.txt", "symmetry": "P1", "comment": null, "user": 425 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/rc01_6iVq9ds_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 0.935, "p_value": 0.0, "fit_residual_plot": "rc01_6iVq9ds_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFD4_fit2.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/rc01_KqVj408.log", "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 the Ycg1-Brn1 complex 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 0.5 and 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 concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.", "tags": [], "intensity_unit": null, "experimental_mw": 138.0, "experimental_mw_error": null, "guinier_i0_mw": 122.0, "guinier_i0_mw_error": null, "porod_mw": 144.0, "porod_mw_error": null, "pddf_i0": 9503.0, "pddf_i0_error": null, "guinier_i0": 9640.0, "guinier_i0_error": 55.0, "pddf_rg": 4.186, "pddf_rg_error": null, "guinier_rg": 4.25, "guinier_rg_error": 0.1, "pddf_dmax": 13.73, "pddf_dmax_error": null, "porod_volume": 230.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 24, "guinier_point_last": 122, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDFD4_datloglog_img.png", "symmetry": null, "last_modified": "2023-06-21T07:56:39.492710+02:00", "bragg_peak": [] }