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{
"code": "SASDVM9",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/A",
"project": {
"title": "Histone modification-driven structural remodeling unleashes DNMT3B in DNA methylation.",
"publication": {
"title": "Histone modification-driven structural remodeling unleashes DNMT3B in DNA methylation.",
"author_list": "Cho CC, Huang HH, Jiang BC, Yang WZ, Chen YN, Yuan HS",
"journal": "Sci Adv",
"doi": "10.1126/sciadv.adu8116",
"pmid": "40138405",
"published_date": "2025 Mar 28"
},
"status": "released",
"submitted_date": "2024-11-09",
"released_date": "2025-01-25"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDVM9.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVM9.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVM9_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVM9_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVM9_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVM9_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVM9.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Eiger X 1M and Eiger X 9M",
"resolution": 75.0
},
"name": "Taiwan Photon Source, NSRRC",
"city": "Hsinchu",
"country": "Taiwan",
"beamline_name": "13A",
"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": "Histone H3.3",
"short_name": "H3.3",
"sequence": ">\r\nMARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPH",
"organism": "Homo sapiens",
"uniprot_code": "P84243",
"uniprot_range_first": 1,
"uniprot_range_last": 40,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTE\nLLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTI\nMPKDIQLARRIRGERA",
"mw": 4.189,
"total_mw": 8.378,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": ""
},
{
"long_name": "DNA methyltransferase 3-like (178-379)",
"short_name": "DNMT3L (178-379)",
"sequence": "GHMFETVPVWRRQPVRVLSLFEDIKKELTSLGFLESGSDPGQLKHVVDVTDTVRKDVEEWGPFDLVYGATPPLGHTCDRPPSWYLFQFHRLLQYARPKPGSPRPFFWMFVDNLVLNKEDLDVASRFLEMEPVTIPDVHGGSLQNAVRVWSNIPAIRSRHWALVSEEELSLLAQNKQSSKLAAKWPTKLVKNCFLPLREYFKYFS",
"organism": "Homo sapiens",
"uniprot_code": "Q9UJW3",
"uniprot_range_first": 178,
"uniprot_range_last": 379,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MAAIPALDPEAEPSMDVILVGSSELSSSVSPGTGRDLIAYEVKANQRNIEDICICCGSLQ\nVHTQHPLFEGGICAPCKDKFLDALFLYDDDGYQSYCSICCSGETLLICGNPDCTRCYCFE\nCVDSLVGPGTSGKVHAMSNWVCYLCLPSSRSGLLQRRRKWRSQLKAFYDRESENPLEMFE\nTVPVWRRQPVRVLSLFEDIKKELTSLGFLESGSDPGQLKHVVDVTDTVRKDVEEWGPFDL\nVYGATPPLGHTCDRPPSWYLFQFHRLLQYARPKPGSPRPFFWMFVDNLVLNKEDLDVASR\nFLEMEPVTIPDVHGGSLQNAVRVWSNIPAIRSRHWALVSEEELSLLAQNKQSSKLAAKWP\nTKLVKNCFLPLREYFKYFSTELTSSL",
"mw": 23.596,
"total_mw": 47.192,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": ""
},
{
"long_name": "DNA methyltransferase 3 beta (413-853)",
"short_name": "DNMT3B (412-853)",
"sequence": "EDQSREQMASDVANNKSSLEDGCLSCGRKNPVSFHPLFEGGLCQTCRDRFLELFYMYDDDGYQSYCTVCCEGRELLLCSNTSCCRCFCVECLEVLVGTGTAAEAKLQEPWSCYMCLPQRCHGVLRRRKDWNVRLQAFFTSDTGLEYEAPKLYPAIPAARRRPIRVLSLFDGIATGYLVLKELGIKVGKYVASEVCEESIAVGTVKHEGNIKYVNDVRNITKKNIEEWGPFDLVIGGSPCNDLSNVNPARKGLYEGTGRLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPVMIDAIKVSAAHRARYFWGNLPGMNRPVIASKNDKLELQDCLEYNRIAKLKKVQTITTKSNSIKQGKNQLFPVVMNGKEDVLWCTELERIFGFPVHYTDVSNMGRGARQKLLGRSWSVPVIRHLFAPLKDYFACE",
"organism": "Homo sapiens",
"uniprot_code": "Q9UBC3",
"uniprot_range_first": 413,
"uniprot_range_last": 853,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MKGDTRHLNGEEDAGGREDSILVNGACSDQSSDSPPILEAIRTPEIRGRRSSSRLSKREV\nSSLLSYTQDLTGDGDGEDGDGSDTPVMPKLFRETRTRSESPAVRTRNNNSVSSRERHRPS\nPRSTRGRQGRNHVDESPVEFPATRSLRRRATASAGTPWPSPPSSYLTIDLTDDTEDTHGT\nPQSSSTPYARLAQDSQQGGMESPQVEADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWP\nAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRK\nAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQPVVNKS\nKVRRAGSRKLESRKYENKTRRRTADDSATSDYCPAPKRLKTNCYNNGKDRGDEDQSREQM\nASDVANNKSSLEDGCLSCGRKNPVSFHPLFEGGLCQTCRDRFLELFYMYDDDGYQSYCTV\nCCEGRELLLCSNTSCCRCFCVECLEVLVGTGTAAEAKLQEPWSCYMCLPQRCHGVLRRRK\nDWNVRLQAFFTSDTGLEYEAPKLYPAIPAARRRPIRVLSLFDGIATGYLVLKELGIKVGK\nYVASEVCEESIAVGTVKHEGNIKYVNDVRNITKKNIEEWGPFDLVIGGSPCNDLSNVNPA\nRKGLYEGTGRLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPVM\nIDAIKVSAAHRARYFWGNLPGMNRPVIASKNDKLELQDCLEYNRIAKLKKVQTITTKSNS\nIKQGKNQLFPVVMNGKEDVLWCTELERIFGFPVHYTDVSNMGRGARQKLLGRSWSVPVIR\nHLFAPLKDYFACE",
"mw": 50.201,
"total_mw": 100.402,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": ""
}
],
"buffer": {
"name": "20 mM Tris, 300 mM NaCl, 1 mM TCEP, 5% glycerol",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 8.0,
"deuteration": null
},
"purity_method": null,
"name": "Human DNA methyltransferase 3 beta DNMT3B (413-853) and DNA methyltransferase 3-like DNMT3L (178-379) in complex with histone H3",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Taipei, Taiwan",
"full_name": "Academia Sinica",
"webpage": "https://www.sinica.edu.tw"
}
],
"contributor_name": "CHAO-CHENG",
"contributor_surname": "CHO",
"orcid": ""
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2022-11-02",
"storage_temperature": 4.0,
"cell_temperature": 10.0,
"exposure_time": 0.2,
"number_of_frames": 113,
"wavelength": 0.0827,
"sample_detector_distance": 2.515,
"concentration_min": null,
"concentration_max": 8.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.067,
"s_max": 5.139,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVM9_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/SASDVM9_fit1_model1.pdb",
"model_mw": null,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 1113
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVM9_fit1_fixed_fit_img.png",
"software": "GASBOR",
"chi_square_value": 1.95,
"p_value": 0.0058,
"fit_residual_plot": "SASDVM9_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVM9_fit1.fir",
"fit_log": null,
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": null,
"experiment_description": null,
"tags": [],
"intensity_unit": null,
"experimental_mw": 156.068,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 115.0,
"porod_mw_error": null,
"pddf_i0": 0.2118,
"pddf_i0_error": null,
"guinier_i0": 0.211114,
"guinier_i0_error": null,
"pddf_rg": 4.58,
"pddf_rg_error": null,
"guinier_rg": 4.485,
"guinier_rg_error": 0.077,
"pddf_dmax": 16.02,
"pddf_dmax_error": null,
"porod_volume": 186.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 50,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDVM9_datloglog_img.png",
"symmetry": null,
"last_modified": "2025-03-30T18:45:24.168653+02:00",
"bragg_peak": []
}
