{ "code": "SASDF52", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/nm", "project": { "title": "Structure, dynamics and roX2-lncRNA binding of tandem double-stranded RNA binding domains dsRBD1,2 of Drosophila helicase Maleless.", "publication": { "title": "Structure, dynamics and roX2-lncRNA binding of tandem double-stranded RNA binding domains dsRBD1,2 of Drosophila helicase Maleless.", "author_list": "Ankush Jagtap PK, Müller M, Masiewicz P, von Bülow S, Hollmann NM, Chen PC, Simon B, Thomae AW, Becker PB, Hennig J", "journal": "Nucleic Acids Res", "doi": "10.1093/nar/gkz125", "pmid": "30805612", "published_date": "2019 May 7" }, "status": "released", "submitted_date": "2019-01-28", "released_date": "2019-02-21" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDF52.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDF52.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF52_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF52_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDF52_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF52_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDF52.sascif", "experiment": { "instrument": { "detector": { "type": "Dectris", "name": "Pilatus 1M", "resolution": 172.0 }, "name": "ESRF", "city": "Grenoble", "country": "France", "beamline_name": "BM29", "beam_geometry": "", "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": "Dosage compensation regulator", "short_name": "MLE", "sequence": "> dsRBD12_single | chain A | 259 aa\r\nGAMDIKSFLYQFCAKSQIEPKFDIRQTGPKNRQRFLCEVRVEPNTYIGVGNSTNKKDAEK\r\nNACRDFVNYLVRVGKLNTNDVPADAGASGGGPRTGLEGAGMAGGSGQQKRVFDGQSGPQD\r\nLGEAYRPLNHDGGDGGNRYSVIDRIQEQRDMNEAEAFDVNAAIHGNWTIENAKERLNIYK\r\nQTNNIRDDYKYTPVGPEHARSFLAELSIYVPALNRTVTARESGSNKKSASKSCALSLVRQ\r\nLFHLNVIEPFSGTLKKKKD", "organism": "Drosophila melanogaster", "uniprot_code": "P24785", "uniprot_range_first": 1, "uniprot_range_last": 257, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MDIKSFLYQFCAKSQIEPKFDIRQTGPKNRQRFLCEVRVEPNTYIGVGNSTNKKDAEKNA\nCRDFVNYLVRVGKLNTNDVPADAGASGGGPRTGLEGAGMAGGSGQQKRVFDGQSGPQDLG\nEAYRPLNHDGGDGGNRYSVIDRIQEQRDMNEAEAFDVNAAIHGNWTIENAKERLNIYKQT\nNNIRDDYKYTPVGPEHARSFLAELSIYVPALNRTVTARESGSNKKSASKSCALSLVRQLF\nHLNVIEPFSGTLKKKKDEQLKPYPVKLSPNLINKIDEVIKGLDLPVVNPRNIKIELDGPP\nIPLIVNLSRIDSSQQDGEKRQESSVIPWAPPQANWNTWHACNIDEGELATTSIDDLSMDY\nERSLRDRRQNDNEYRQFLEFREKLPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQY\nILDDYICSGQGGYANIYVTQPRRISAISVAERVARERCEQLGDTVGYSVRFESVFPRPYG\nAILFCTVGVLLRKLEAGLRGVSHIIVDEIHERDVNSDFLLVILRDMVDTYPDLHVILMSA\nTIDTTKFSKYFGICPVLEVPGRAFPVQQFFLEDIIQMTDFVPSAESRRKRKEVEDEEQLL\nSEDKDEAEINYNKVCEDKYSQKTRNAMAMLSESDVSFELLEALLMHIKSKNIPGAILVFL\nPGWNLIFALMKFLQNTNIFGDTSQYQILPCHSQIPRDEQRKVFEPVPEGVTKIILSTNIA\nETSITIDDIVFVIDICKARMKLFTSHNNLTSYATVWASKTNLEQRKGRAGRVRPGFCFTL\nCSRARFQALEDNLTPEMFRTPLHEMALTIKLLRLGSIHHFLSKALEPPPVDAVIEAEVLL\nREMRCLDANDELTPLGRLLARLPIEPRLGKMMVLGAVFGCADLMAIMASYSSTFSEVFSL\nDIGQRRLANHQKALSGTKCSDHVAMIVASQMWRREKQRGEHMEARFCDWKGLQMSTMNVI\nWDAKQQLLDLLQQAGFPEECMISHEVDERIDGDDPVLDVSLALLCLGLYPNICVHKEKRK\nVLTTESKAALLHKTSVNCSNLAVTFPYPFFVFGEKIRTRAVSCKQLSMVSPLQVILFGSR\nKIDLAANNIVRVDNWLNFDIEPELAAKIGALKPALEDLITVACDNPSDILRLEEPYAQLV\nKVVKDLCVKSAGDFGLQRESGILPHQSRQFSDGGGPPKRGRFETGRFTNSSFGRRGNGRT\nFGGGYGNNGGGYGNNGGGYGNIGGGYGNNAGGYGNNGGYGNNGGGYRNNGGGYGNNGGGY\nGNKRGGFGDSFESNRGSGGGFRNGDQGGRWGNF", "mw": 28.549, "total_mw": 28.549, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM NaPO4, 200 mM NaCl, 1 mM DTT", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 6.5, "deuteration": null }, "purity_method": null, "name": "dsRBD1 and dsRBD2 domains of Drosophila helicase dosage compensation regulator, MLE", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "EMBL", "address": "Heidelberg, Germany", "full_name": "European Molecular Biology Laboratory (EMBL) - Heidelberg", "webpage": "https://www.embl.de/" } ], "contributor_name": "Po-chia", "contributor_surname": "Chen", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2016-11-29", "storage_temperature": null, "cell_temperature": 20.0, "exposure_time": 1.0, "number_of_frames": 10, "wavelength": 0.09919, "sample_detector_distance": 2.867, "concentration_min": 5.0, "concentration_max": 5.0, "sample_volume": null, "flow_rate": null, "s_min": 0.035, "s_max": 4.944, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF52_fit1_model1_img.png", "software": "EOM/RANCH", "pdb_link": [], "model_title": null, "type_of_model": "mix", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDF52_fit1_model1.pdb", "model_mw": 29.13, "bead_radius": 1.9, "log": null, "symmetry": null, "comment": null, "user": 297 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF52_fit1_model2_img.png", "software": "EOM/RANCH", "pdb_link": [], "model_title": null, "type_of_model": "mix", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDF52_fit1_model2.pdb", "model_mw": 29.13, "bead_radius": 1.9, "log": null, "symmetry": null, "comment": null, "user": 297 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF52_fit1_model3_img.png", "software": "EOM/RANCH", "pdb_link": [], "model_title": null, "type_of_model": "mix", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDF52_fit1_model3.pdb", "model_mw": 29.13, "bead_radius": 1.9, "log": null, "symmetry": null, "comment": null, "user": 297 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF52_fit1_model4_img.png", "software": "EOM/RANCH", "pdb_link": [], "model_title": null, "type_of_model": "mix", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDF52_fit1_model4.pdb", "model_mw": 29.13, "bead_radius": 1.9, "log": null, "symmetry": null, "comment": null, "user": 297 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF52_fit1_fixed_fit_img.png", "software": "EOM/GAJOE", "chi_square_value": 2.089, "p_value": 0.0, "fit_residual_plot": "SASDF52_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF52_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/logFile_001_1_uBn8rj9.log", "software_version": null, "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": "Construct contains an additional two amino acids (Gly-Ala) at the N-terminus as a remaining product the TEV-protease cleavage.\r\nThe data displayed in this entry consists of merged data from three replicates of equal sample concentration (5.0 mg/ml). Thus, an effective total of 30 frames x 1s exposures is collated for this curve. The data were merged using Primus and datmerge of the ATSAS 2.8.4-1 package maintained by SBGrid.", "experiment_description": "Synchrotron SAXS data from solutions of the dsRBD1 and dsRBD2 domains of Drosophila helicase dosage compensation regulator, MLE, in 20 mM NaPO4, 200 mM NaCl, 1 mM DTT, pH 6.5 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.09919 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). A solute concentration of 5 mg/ml was measured at 20°C. 10 successive 1 second frames were collected per sample (three replicates total). 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": 14.8, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 14.0, "porod_mw_error": null, "pddf_i0": 66.44, "pddf_i0_error": null, "guinier_i0": 66.26, "guinier_i0_error": 0.13, "pddf_rg": 3.337, "pddf_rg_error": null, "guinier_rg": 3.23, "guinier_rg_error": 0.13, "pddf_dmax": 12.5, "pddf_dmax_error": null, "porod_volume": 22.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 6, "guinier_point_last": 60, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDF52_datloglog_img.png", "symmetry": null, "last_modified": "2020-08-28T15:27:32.015613+02:00", "bragg_peak": [] }