{ "code": "SASDBY7", "status": "Published", "type_of_curve": "Extrapolated to infinite dilution", "angular_unit": "1/nm", "project": { "title": "Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes.", "publication": { "title": "Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes.", "author_list": "Sundaramoorthy R, Hughes AL, Singh V, Wiechens N, Ryan DP, El-Mkami H, Petoukhov M, Svergun DI, Treutlein B, Quack S, Fischer M, Michaelis J, Böttcher B, Norman DG, Owen-Hughes T", "journal": "Elife", "doi": "10.7554/eLife.22510", "pmid": "28332978", "published_date": "2017 Mar 23" }, "status": "released", "submitted_date": "2016-11-26", "released_date": "2017-05-02" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBY7.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBY7.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBY7_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBY7_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBY7_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBY7_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBY7.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 2M", "resolution": null }, "name": "DORIS III, DESY", "city": "Hamburg", "country": "Germany", "beamline_name": "EMBL X33", "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": "chromodomain helicase DNA binding domain", "short_name": "Chd1", "sequence": "MAAKDISTEV LQNPELYGLR RSHRAAAHQQ NYFNDSDDED DEDNIKQSRR KRMTTIEDDE \r\n DEFEDEEGEE DSGEDEDEED FEEDDDYYGS PIKQNRSKPK SRTKSKSKSK PKSQSEKQST \r\n VKIPTRFSNR QNKTVNYNID YSDDDLLESE DDYGSEEALS EENVHEASAN PQPEDFHGID \r\n IVINHRLKTS LEEGKVLEKT VPDLNNCKEN YEFLIKWTDE SHLHNTWETY ESIGQVRGLK \r\n RLDNYCKQFI IEDQQVRLDP YVTAEDIEIM DMERERRLDE FEEFHVPERI IDSQRASLED \r\n GTSQLQYLVK WRRLNYDEAT WENATDIVKL APEQVKHFQN RENSKILPQY SSNYTSQRPR \r\n FEKLSVQPPF IKGGELRDFQ LTGINWMAFL WSKGDNGILA DEMGLGKTVQ TVAFISWLIF \r\n ARRQNGPHII VVPLSTMPAW LDTFEKWAPD LNCICYMGNQ KSRDTIREYE FYTNPRAKGK \r\n KTMKFNVLLT TYEYILKDRA ELGSIKWQFM AVDEAHRLKN AESSLYESLN SFKVANRMLI \r\n TGTPLQNNIK ELAALVNFLM PGRFTIDQEI DFENQDEEQE EYIHDLHRRI QPFILRRLKK \r\n DVEKSLPSKT ERILRVELSD VQTEYYKNIL TKNYSALTAG AKGGHFSLLN IMNELKKASN \r\n HPYLFDNAEE RVLQKFGDGK MTRENVLRGL IMSSGKMVLL DQLLTRLKKD GHRVLIFSQM \r\n VRMLDILGDY LSIKGINFQR LDGTVPSAQR RISIDHFNSP DSNDFVFLLS TRAGGLGINL \r\n MTADTVVIFD SDWNPQADLQ AMARAHRIGQ KNHVMVYRLV SKDTVEEEVL ERARKKMILE \r\n YAIISLGVTD GNKYTKKNEP NAGELSAILK FGAGNMFTAT DNQKKLEDLN LDDVLNHAED \r\n HVTTPDLGES HLGGEEFLKQ FEVTDYKADI DWDDIIPEEE LKKLQDEEQK RKDEEYVKEQ \r\n LEMMNRRDNA LKKIKNSVNG DGTAANSDSD DDSTSRSSRR RARANDMDSI", "organism": "Saccharomyces cerevisiae", "uniprot_code": "P32657", "uniprot_range_first": 1, "uniprot_range_last": 1010, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MAAKDISTEVLQNPELYGLRRSHRAAAHQQNYFNDSDDEDDEDNIKQSRRKRMTTIEDDE\nDEFEDEEGEEDSGEDEDEEDFEEDDDYYGSPIKQNRSKPKSRTKSKSKSKPKSQSEKQST\nVKIPTRFSNRQNKTVNYNIDYSDDDLLESEDDYGSEEALSEENVHEASANPQPEDFHGID\nIVINHRLKTSLEEGKVLEKTVPDLNNCKENYEFLIKWTDESHLHNTWETYESIGQVRGLK\nRLDNYCKQFIIEDQQVRLDPYVTAEDIEIMDMERERRLDEFEEFHVPERIIDSQRASLED\nGTSQLQYLVKWRRLNYDEATWENATDIVKLAPEQVKHFQNRENSKILPQYSSNYTSQRPR\nFEKLSVQPPFIKGGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIF\nARRQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNPRAKGK\nKTMKFNVLLTTYEYILKDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLI\nTGTPLQNNIKELAALVNFLMPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFILRRLKK\nDVEKSLPSKTERILRVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASN\nHPYLFDNAEERVLQKFGDGKMTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQM\nVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINL\nMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEVLERARKKMILE\nYAIISLGVTDGNKYTKKNEPNAGELSAILKFGAGNMFTATDNQKKLEDLNLDDVLNHAED\nHVTTPDLGESHLGGEEFLKQFEVTDYKADIDWDDIIPEEELKKLQDEEQKRKDEEYVKEQ\nLEMMNRRDNALKKIKNSVNGDGTAANSDSDDDSTSRSSRRRARANDMDSIGESEVRALYK\nAILKFGNLKEILDELIADGTLPVKSFEKYGETYDEMMEAAKDCVHEEEKNRKEILEKLEK\nHATAYRAKLKSGEIKAENQPKDNPLTRLSLKKREKKAVLFNFKGVKSLNAESLLSRVEDL\nKYLKNLINSNYKDDPLKFSLGNNTPKPVQNWSSNWTKEEDEKLLIGVFKYGYGSWTQIRD\nDPFLGITDKIFLNEVHNPVAKKSASSSDTTPTPSKKGKGITGSSKKVPGAIHLGRRVDYL\nLSFLRGGLNTKSPSADIGSKKLPTGPSKKRQRKPANHSKSMTPEITSSEPANGPPSKRMK\nALPKGPAALINNTRLSPNSPTPPLKSKVSRDNGTRQSSNPSSGSAHEKEYDSMDEEDCRH\nTMSAIRTSLKRLRRGGKSLDRKEWAKILKTELTTIGNHIESQKGSSRKASPEKYRKHLWS\nYSANFWPADVKSTKLMAMYDKITESQKK", "mw": 116.922, "total_mw": 116.922, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50mM Hepes 150mM NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "N-terminal and chromo-ATPase domains of chromo domain-containing protein 1 (Chd1: 1-1010)", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Dundee, UK", "full_name": "University of Dundee", "webpage": "https://www.dundee.ac.uk/" } ], "contributor_name": "Ramasubramanian", "contributor_surname": "Sundaramoorthy", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2008-11-30", "storage_temperature": 10.0, "cell_temperature": 10.0, "exposure_time": 120.0, "number_of_frames": null, "wavelength": 0.154, "sample_detector_distance": 5.0, "concentration_min": 0.6, "concentration_max": 9.8, "sample_volume": null, "flow_rate": null, "s_min": 0.073, "s_max": 4.945, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBY7_fit1_model1_img.png", "software": "GASBOR", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "2.3i", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDBY7_fit1_model1.pdb", "model_mw": null, "bead_radius": 1.9, "log": null, "symmetry": "C1", "comment": "", "user": 184 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBY7_fit1_fit_img.png", "software": "GASBOR", "chi_square_value": 5.4, "p_value": 0.0, "fit_residual_plot": "SASDBY7_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBY7_fit1.fir", "fit_log": null, "software_version": "", "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": null, "i0_calibration_standard": null, "description": "The protein fragment 1-1010 encompassing the N-terminal and chromo-ATPase domains of Saccharomyces cerevisiae Chd1.", "experiment_description": "Synchrotron SAXS data from solutions of the N-terminal-chromo-ATPase domains of chromo domain-containing protein 1 (Chd1: 1-1010) in 50mM HEPES, 150mM NaCl, pH 7.5 were collected at the X33 beam line on the DORIS III storage ring (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 5 m and at a wavelength of λ = 0.154 nm (I(s) vs s, where s = 4πsin θ/λ and 2θ is the scattering angle). Solute concentrations ranging between 0.6 and 9.8 mg/ml were measured at 10°C. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the different curves were scaled for protein concentration. 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": [ "X33" ], "intensity_unit": null, "experimental_mw": 120.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 1.22, "pddf_i0_error": 0.001, "guinier_i0": 1.36, "guinier_i0_error": 0.0035, "pddf_rg": 4.07, "pddf_rg_error": 0.002, "guinier_rg": 4.53, "guinier_rg_error": 0.01, "pddf_dmax": 12.0, "pddf_dmax_error": null, "porod_volume": 228.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 7, "guinier_point_last": 94, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDBY7_datloglog_img.png", "symmetry": null, "last_modified": "2023-05-25T11:22:08.798758+02:00", "bragg_peak": [] }