SASDVK9

Pro-Trp-Trp-Pro (PWWP) domain from human DNA (cytosine-5)-methyltransferase 3B (DNMT3B) in complex with histone H3

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Single concentration 最后更新:2025-03-30T18:45:23.911685+02:00
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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Pro-Trp-Trp-Pro (PWWP) domain from human DNA (cytosine-5)-methyltransferase 3B (DNMT3B) in complex with histone H3

浓度— – 10.0 缓冲液 / pH20 mM Tris, 300 mM NaCl, 1 mM TCEP, 5% glycerol / 8.0
实验温度10.0 设备 / 束线Taiwan Photon Source, NSRRC / 13A
波长0.0827 nm曝光0.2 s × 107

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
Histone H3.3
查看序列
>MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPH
proteinHomo saP842431–40monomer分子数 14.189 kDa
DNA (cytosine-5)-methyltransferase 3B Pro-Trp-Trp-Pro (PWWP) domain
查看序列
EADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQP
proteinHomo sapiensQ9UBC3206–355monomer分子数 116.677 kDa

实验曲线

曲线点数 / 列q 范围误差质量负强度点来源文件
1501[3]0.007389–1.166796 1/A含误差列缺失 00sasbdb/entries/k9/sasdvk9/source/SASDVK9.dat
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2. SASBDB 报告的指标 Reported Results

指标方法数值误差单位
dmaxP(r)7.35—Å
i0Guinier0.0340232—1/cm
i0P(r)0.03415—1/cm
mwExperimental20.934—kDa
mwPorod12.0—kDa
porod_volumePorod19.0—ų
rgGuinier1.750.057Å
rgP(r)1.78—Å

这些数值是 SASBDB 来源记录,不是 SAXSdb 对实验曲线重新计算的结果。

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3. 来源拟合与模型 Source Fits & Models

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4. 来源文件索引 Source Files

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5. 实验说明与论文 Experiment & Publication

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6. 完整来源记录 Complete Source Record

下列内容直接来自 SASBDB 条目。字段没有值时显示“—”;未声明的单位不会由 SAXSdb 猜测。

打开 SASBDB 原始条目

缓冲液与样品属性

缓冲液名称20 mM Tris, 300 mM NaCl, 1 mM TCEP, 5% glycerol缓冲液浓度—
pH8.0添加剂—
缓冲液说明—
纯度测定方法—消光系数—
吸收值—散射对比度—
比体积 / 干体积— / —混合物 / 氘代— / —

采集条件与仪器

测量日期2024-09-17储存 / 测量温度4.0 / 10.0
曝光时间0.2帧数107
波长0.0827样品-探测器距离2.507
光源X-ray synchrotron探测器Eiger X 1M and Eiger X 9M
机构 / 束线Taiwan Photon Source, NSRRC / 13A · Hsinchu, Taiwan
q 范围0.074 – 11.668样品体积 / 流速— / —

SASBDB 原始图

实验 I(q)
实验 I(q)
实验 I(q) log-log
实验 I(q) log-log
Guinier 图
Guinier 图
Kratky 图
Kratky 图
P(r) 图
P(r) 图

可下载文件

类别文件状态大小校验值下载与查看
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full_entry_zipsasbdb/entries/k9/sasdvk9/source/SASDVK9.zipdownloaded25904c7644c60e4f22b3dbc72cd3147205f5a366b142d35cdc4d6c03a198501c0ca6f下载查看原文件源站
pddfsasbdb/entries/k9/sasdvk9/source/SASDVK9.outdownloaded308308695c968e2145a116209a58d8a3002efcc264b231d0ec8cc730360ba37d542c6下载查看原文件源站
sascifsasbdb/entries/k9/sasdvk9/source/SASDVK9.sascifnot_available——下载查看原文件源站
summarysasbdb/entries/k9/sasdvk9/source/summary.jsondownloaded81343273a2863aab7d010f1d9317cb46e91929d929683827cd5ac55f0373bf170592下载查看原文件源站
curve:来源记录
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full_entry_zip:来源记录与 ZIP 内部目录(4 项)
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pddf:来源记录
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sascif:来源记录
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summary:来源记录
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全部来源字段(无筛选)

这里自动展开来源记录中的每一个字段,包括空值、列表成员和页面上方已展示过的字段。

summary.json:173 个字段值
字段路径原始值
codeSASDVK9
statusPublished
type_of_curveSingle concentration
angular_unit1/A
project.titleHistone modification-driven structural remodeling unleashes DNMT3B in DNA methylation.
project.publication.titleHistone modification-driven structural remodeling unleashes DNMT3B in DNA methylation.
project.publication.author_listCho CC, Huang HH, Jiang BC, Yang WZ, Chen YN, Yuan HS
project.publication.journalSci Adv
project.publication.doi10.1126/sciadv.adu8116
project.publication.pmid40138405
project.publication.published_date2025 Mar 28
project.statusreleased
project.submitted_date2024-11-09
project.released_date2025-01-25
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDVK9.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDVK9.dat
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intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVK9_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVK9_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVK9_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDVK9.sascif
experiment.instrument.detector.typenull
experiment.instrument.detector.nameEiger X 1M and Eiger X 9M
experiment.instrument.detector.resolution75.0
experiment.instrument.nameTaiwan Photon Source, NSRRC
experiment.instrument.cityHsinchu
experiment.instrument.countryTaiwan
experiment.instrument.beamline_name13A
experiment.instrument.beam_geometrynull
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourcenull
experiment.instrument.line_collimationnull
experiment.instrument.sample_path_lengthnull
experiment.instrument.line_collimation_slitlengthnull
experiment.instrument.line_collimation_integrationwidthnull
experiment.instrument.xray_energynull
experiment.instrument.beam_profile_ahnull
experiment.instrument.beam_profile_alnull
experiment.sample.molecule[0].long_nameHistone H3.3
experiment.sample.molecule[0].short_nameH3.3
experiment.sample.molecule[0].sequence> MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPH
experiment.sample.molecule[0].organismHomo sa
experiment.sample.molecule[0].uniprot_codeP84243
experiment.sample.molecule[0].uniprot_range_first1
experiment.sample.molecule[0].uniprot_range_last40
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTE LLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTI MPKDIQLARRIRGERA
experiment.sample.molecule[0].mw4.189
experiment.sample.molecule[0].total_mw4.189
experiment.sample.molecule[0].number_molecules1
experiment.sample.molecule[0].complex_stateFalse
experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
experiment.sample.molecule[0].molecule_description
experiment.sample.molecule[1].long_nameDNA (cytosine-5)-methyltransferase 3B Pro-Trp-Trp-Pro (PWWP) domain
experiment.sample.molecule[1].short_nameDNMT3B PWWP domain
experiment.sample.molecule[1].sequenceEADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQP
experiment.sample.molecule[1].organismHomo sapiens
experiment.sample.molecule[1].uniprot_codeQ9UBC3
experiment.sample.molecule[1].uniprot_range_first206
experiment.sample.molecule[1].uniprot_range_last355
experiment.sample.molecule[1].oligomerizationmonomer
experiment.sample.molecule[1].molecular_typeprotein
experiment.sample.molecule[1].uniprot_sequenceMKGDTRHLNGEEDAGGREDSILVNGACSDQSSDSPPILEAIRTPEIRGRRSSSRLSKREV SSLLSYTQDLTGDGDGEDGDGSDTPVMPKLFRETRTRSESPAVRTRNNNSVSSRERHRPS PRSTRGRQGRNHVDESPVEFPATRSLRRRATASAGTPWPSPPSSYLTIDLTDDTEDTHGT PQSSSTPYARLAQDSQQGGMESPQVEADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWP AMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRK AMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQPVVNKS KVRRAGSRKLESRKYENKTRRRTADDSATSDYCPAPKRLKTNCYNNGKDRGDEDQSREQM ASDVANNKSSLEDGCLSCGRKNPVSFHPLFEGGLCQTCRDRFLELFYMYDDDGYQSYCTV CCEGRELLLCSNTSCCRCFCVECLEVLVGTGTAAEAKLQEPWSCYMCLPQRCHGVLRRRK DWNVRLQAFFTSDTGLEYEAPKLYPAIPAARRRPIRVLSLFDGIATGYLVLKELGIKVGK YVASEVCEESIAVGTVKHEGNIKYVNDVRNITKKNIEEWGPFDLVIGGSPCNDLSNVNPA RKGLYEGTGRLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPVM IDAIKVSAAHRARYFWGNLPGMNRPVIASKNDKLELQDCLEYNRIAKLKKVQTITTKSNS IKQGKNQLFPVVMNGKEDVLWCTELERIFGFPVHYTDVSNMGRGARQKLLGRSWSVPVIR HLFAPLKDYFACE
experiment.sample.molecule[1].mw16.677
experiment.sample.molecule[1].total_mw16.677
experiment.sample.molecule[1].number_molecules1
experiment.sample.molecule[1].complex_stateFalse
experiment.sample.molecule[1].deuterationnull
experiment.sample.molecule[1].molecule_sourcebiological
experiment.sample.molecule[1].molecule_description
experiment.sample.buffer.name20 mM Tris, 300 mM NaCl, 1 mM TCEP, 5% glycerol
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph8.0
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.namePro-Trp-Trp-Pro (PWWP) domain from human DNA (cytosine-5)-methyltransferase 3B (DNMT3B) in complex with histone H3
experiment.sample.ext_coefficientnull
experiment.sample.contrastnull
experiment.sample.specific_volnull
experiment.sample.dry_volnull
experiment.sample.absorbptionnull
experiment.sample.deuterationnull
experiment.sample.mixturenull
experiment.contributor[0].affiliation[0].short_namenull
experiment.contributor[0].affiliation[0].addressTaipei, Taiwan
experiment.contributor[0].affiliation[0].full_nameAcademia Sinica
experiment.contributor[0].affiliation[0].webpagehttps://www.sinica.edu.tw
experiment.contributor[0].contributor_nameCHAO-CHENG
experiment.contributor[0].contributor_surnameCHO
experiment.contributor[0].orcid
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2024-09-17
experiment.storage_temperature4.0
experiment.cell_temperature10.0
experiment.exposure_time0.2
experiment.number_of_frames107
experiment.wavelength0.0827
experiment.sample_detector_distance2.507
experiment.concentration_minnull
experiment.concentration_max10.0
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.074
experiment.s_max11.668
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].lognull
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fits[0].models[0].commentnull
fits[0].models[0].user1113
fits[0].fit_unit1/A
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fits[0].softwareGASBOR
fits[0].chi_square_value1.48
fits[0].p_value0.0
fits[0].fit_residual_plotSASDVK9_fit1_fitresiduals_img.png
fits[0].fit_datahttps://www.sasbdb.org/media/fitting_files/SASDVK9_fit1.fir
fits[0].fit_lognull
fits[0].software_versionnull
fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionnull
tags[]
intensity_unit1/cm
experimental_mw20.934
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw12.0
porod_mw_errornull
pddf_i00.03415
pddf_i0_errornull
guinier_i00.0340232
guinier_i0_errornull
pddf_rg1.78
pddf_rg_errornull
guinier_rg1.75
guinier_rg_error0.057
pddf_dmax7.35
pddf_dmax_errornull
porod_volume19.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first7
guinier_point_last133
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDVK9_datloglog_img.png
symmetrynull
last_modified2025-03-30T18:45:23.911685+02:00
bragg_peak[]
manifest.json:34 个字段值
字段路径原始值
codeSASDVK9
statussuccess
started_at2026-08-11T16:34:36.354531+00:00
finished_at2026-08-11T16:34:43.276762+00:00
source_last_modified2025-03-30T18:45:23.911685+02:00
files[0].statusdownloaded
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查看完整 summary.json 原文
{
  "code": "SASDVK9",
  "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"
  },
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  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVK9.sascif",
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        "name": "Eiger X 1M and Eiger X 9M",
        "resolution": 75.0
      },
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      "city": "Hsinchu",
      "country": "Taiwan",
      "beamline_name": "13A",
      "beam_geometry": null,
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    "sample": {
      "molecule": [
        {
          "long_name": "Histone H3.3",
          "short_name": "H3.3",
          "sequence": ">\r\nMARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPH",
          "organism": "Homo sa",
          "uniprot_code": "P84243",
          "uniprot_range_first": 1,
          "uniprot_range_last": 40,
          "oligomerization": "monomer",
          "molecular_type": "protein",
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}
查看完整 manifest.json 原文
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