SASDBU4

Vaccinia primase D5 protein fragment containing the D5N and helicase domain

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Single concentration 最后更新:2019-12-06T13:07:15.624532+01:00
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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Vaccinia primase D5 protein fragment containing the D5N and helicase domain

浓度1.42 – 2.2 mg/ml缓冲液 / pH20 mM Tris 150 mM NaCL 5% glycerol 1mM DTT / 7.0
实验温度20.0 设备 / 束线ESRF / BM29
波长0.93 nm曝光2.0 s × 2000

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
Primase D5 protein fragment containing the D5N and helicase domain
查看序列
GAMGNKLFNIAQRILDTNSVLLTERGDYIVWINNSWKFNSEEPLITKLILSIRHQLPKEYSSELLCPRKRKTVEANIRDMLVDSVETDTYPDKLPFKNGVLDLVDGMFYSGDDAKKYTCTVSTGFKFDDTKFVEDSPEMEELMNIINDIQPLTDENKKNRELYEKTLSSCLCGATKGCLTFFFGETATGKSTTKRLLKSAIGDLFVETGQTILTDVLDKGPNPFIANMHLKRSVFCSELPDFACSGSKKIRSDNIKKLTEPCVIGRPCFSNKINNRNHATIIIDTNYKPVFDRIDNALMRRIAVVRFRTHFSQPSGREAAENNDAYDKVKLLDEGLDGKIQNNRYRFAFLYLLVKWYKKYHVPIMKLYPTPEEIPDFAFYLKIGTLLVSSSVKHIPLMTDLSKKGYILYDNVVTLPLTTFQQKISKYFNSRLFGHDIESFINRHKKFANVSDEYLQYIFIEDISSP
proteinVaccinia virusP21010323–785hexamer分子数 653.48 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
11018[3]0.1546941–4.969332 1/nm含误差列缺失 014sasbdb/entries/u4/sasdbu4/source/SASDBU4.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)14.5—nm
i0Guinier29.50.04—
i0P(r)29.00.04—
mwExperimental345.0—kDa
porod_volumePorod570.0—nm³
rgGuinier4.80.03nm
rgP(r)4.70.006nm

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 150 mM NaCL 5% glycerol 1mM DTT缓冲液浓度20.0 mM
pH7.0添加剂150 mM NaCL, 5% glycerol, 1mM DTT
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2014-09-26储存 / 测量温度20.0 / 20.0
曝光时间2.0帧数2000
波长0.93样品-探测器距离2.43
光源X-ray synchrotron探测器Pilatus 1M
机构 / 束线ESRF / BM29 · Grenoble, France
q 范围0.155 – 4.969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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pddfsasbdb/entries/u4/sasdbu4/source/SASDBU4.outdownloaded267466fded6928f38ab93e0ce6915e9c8c2aa0eee9d7cf6884d7ffe2979b142e08711下载查看原文件源站
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summarysasbdb/entries/u4/sasdbu4/source/summary.jsondownloaded8062d054120fcdd5a84183fba650933b58a8c587accddc7c77539f5ae75ac8000a6a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:153 个字段值
字段路径原始值
codeSASDBU4
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleDomain Organization of Vaccinia Virus Helicase-Primase D5.
project.publication.titleDomain Organization of Vaccinia Virus Helicase-Primase D5.
project.publication.author_listHutin S, Ling WL, Round A, Effantin G, Reich S, Iseni F, Tarbouriech N, Schoehn G, Burmeister WP
project.publication.journalJ Virol
project.publication.doi10.1128/JVI.00044-16
project.publication.pmid26912611
project.publication.published_date2016 May
project.statusreleased
project.submitted_date2016-04-11
project.released_date2016-04-11
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDBU4.out
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experiment.instrument.detector.typeDectris
experiment.instrument.detector.namePilatus 1M
experiment.instrument.detector.resolution172.0
experiment.instrument.nameESRF
experiment.instrument.cityGrenoble
experiment.instrument.countryFrance
experiment.instrument.beamline_nameBM29
experiment.instrument.beam_geometry
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_namePrimase D5 protein fragment containing the D5N and helicase domain
experiment.sample.molecule[0].short_nameVaccinia D5 323-785
experiment.sample.molecule[0].sequenceGAMGNKLFNI AQRILDTNSV LLTERGDYIV WINNSWKFNS EEPLITKLIL SIRHQLPKEY SSELLCPRKR KTVEANIRDM LVDSVETDTY PDKLPFKNGV LDLVDGMFYS GDDAKKYTCT VSTGFKFDDT KFVEDSPEME ELMNIINDIQ PLTDENKKNR ELYEKTLSSC LCGATKGCLT FFFGETATGK STTKRLLKSA IGDLFVETGQ TILTDVLDKG PNPFIANMHL KRSVFCSELP DFACSGSKKI RSDNIKKLTE PCVIGRPCFS NKINNRNHAT IIIDTNYKPV FDRIDNALMR RIAVVRFRTH FSQPSGREAA ENNDAYDKVK LLDEGLDGKI QNNRYRFAFL YLLVKWYKKY HVPIMKLYPT PEEIPDFAFY LKIGTLLVSS SVKHIPLMTD LSKKGYILYD NVVTLPLTTF QQKISKYFNS RLFGHDIESF INRHKKFANV SDEYLQYIFI EDISSP
experiment.sample.molecule[0].organismVaccinia virus
experiment.sample.molecule[0].uniprot_codeP21010
experiment.sample.molecule[0].uniprot_range_first323
experiment.sample.molecule[0].uniprot_range_last785
experiment.sample.molecule[0].oligomerizationhexamer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMDAAIRGNDVIFVLKTIGVPSACRQNEDPRFVEAFKCDELKRYIDNNPECTLFESLRDEE AYSIVRIFMDVDLDACLDEIDYLTAIQDFIIEVSNCVARFAFTECGAIHENVIKSMRSNF SLTKSTNRDKTSFHIIFLDTYTTMDTLIAMKRTLLELSRSSENPLTRSIDTAVYRRKTTL RVVGTRKNPNCDTIHVMQPPHDNIEDYLFTYVDMNNNSYYFSLQRRLEDLVPDKLWEPGF ISFEDAIKRVSKIFINSIINFNDLDENNFTTVPLVIDYVTPCALCKKRSHKHPHQLSLEN GAIRIYKTGNPHSCKVKIVPLDGNKLFNIAQRILDTNSVLLTERGDYIVWINNSWKFNSE EPLITKLILSIRHQLPKEYSSELLCPRKRKTVEANIRDMLVDSVETDTYPDKLPFKNGVL DLVDGMFYSGDDAKKYTCTVSTGFKFDDTKFVEDSPEMEELMNIINDIQPLTDENKKNRE LYEKTLSSCLCGATKGCLTFFFGETATGKSTTKRLLKSAIGDLFVETGQTILTDVLDKGP NPFIANMHLKRSVFCSELPDFACSGSKKIRSDNIKKLTEPCVIGRPCFSNKINNRNHATI IIDTNYKPVFDRIDNALMRRIAVVRFRTHFSQPSGREAAENNDAYDKVKLLDEGLDGKIQ NNRYRFAFLYLLVKWYKKYHVPIMKLYPTPEEIPDFAFYLKIGTLLVSSSVKHIPLMTDL SKKGYILYDNVVTLPLTTFQQKISKYFNSRLFGHDIESFINRHKKFANVSDEYLQYIFIE DISSP
experiment.sample.molecule[0].mw53.48
experiment.sample.molecule[0].total_mw320.879
experiment.sample.molecule[0].number_molecules6
experiment.sample.molecule[0].complex_stateFalse
experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
experiment.sample.molecule[0].molecule_descriptionnull
experiment.sample.buffer.name20 mM Tris 150 mM NaCL 5% glycerol 1mM DTT
experiment.sample.buffer.concentration_unitmM
experiment.sample.buffer.commentnull
experiment.sample.buffer.additive150 mM NaCL, 5% glycerol, 1mM DTT
experiment.sample.buffer.concentration20.0
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.0
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameVaccinia primase D5 protein fragment containing the D5N and helicase domain
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[]
experiment.contributor[0].contributor_nameStephanie
experiment.contributor[0].contributor_surnameHutin
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitmg/ml
experiment.date2014-09-26
experiment.storage_temperature20.0
experiment.cell_temperature20.0
experiment.exposure_time2.0
experiment.number_of_frames2000
experiment.wavelength0.93
experiment.sample_detector_distance2.43
experiment.concentration_min1.42
experiment.concentration_max2.2
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.155
experiment.s_max4.969
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].softwareDAMMIF
fits[0].models[0].pdb_link[]
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fits[0].models[0].model_mw370.5
fits[0].models[0].bead_radius3.0
fits[0].models[0].lognull
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fits[0].models[0].comment
fits[0].models[0].user124
fits[0].fit_unit1/A
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fits[0].softwarenull
fits[0].chi_square_value1.05
fits[0].p_value4e-06
fits[0].fit_residual_plotSASDBU4_fit1_fitresiduals_img.png
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fits[0].software_versionnull
fits[0].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionnull
i0_calibration_standardnull
descriptionnull
experiment_descriptionX-ray synchrotron radiation scattering data from solutions of the primase D5 protein fragment from Vaccinia virus containing the D5N and helicase domain in 20 mM Tris 150 mM NaCL, 5% glycerol, 1mM DTT pH 7 on the BM29 SAXS beam line at the ESRF (Grenoble, France) using a 2D Photon counting Pilatus 1M-W pixel detector (I(s) vs s; s = 4π sin θ/λ, where 2θ is the scattering angle and λ=0.1 nm). A solute concentration of 1.42 mg/ml was measured using 2000 successive 2 second frames. 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 and averaged.
tags[]
intensity_unitnull
experimental_mw345.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i029.0
pddf_i0_error0.04
guinier_i029.5
guinier_i0_error0.04
pddf_rg4.7
pddf_rg_error0.006
guinier_rg4.8
guinier_rg_error0.03
pddf_dmax14.5
pddf_dmax_errornull
porod_volume570.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first2
guinier_point_last24
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDBU4_datloglog_img.png
symmetrynull
last_modified2019-12-06T13:07:15.624532+01:00
bragg_peak[]
manifest.json:36 个字段值
字段路径原始值
codeSASDBU4
statussuccess
started_at2026-08-11T14:31:22.293885+00:00
finished_at2026-08-11T14:31:30.956311+00:00
source_last_modified2019-12-06T13:07:15.624532+01:00
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查看完整 summary.json 原文
{
  "code": "SASDBU4",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Domain Organization of Vaccinia Virus Helicase-Primase D5.",
    "publication": {
      "title": "Domain Organization of Vaccinia Virus Helicase-Primase D5.",
      "author_list": "Hutin S, Ling WL, Round A, Effantin G, Reich S, Iseni F, Tarbouriech N, Schoehn G, Burmeister WP",
      "journal": "J Virol",
      "doi": "10.1128/JVI.00044-16",
      "pmid": "26912611",
      "published_date": "2016 May"
    },
    "status": "released",
    "submitted_date": "2016-04-11",
    "released_date": "2016-04-11"
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          "long_name": "Primase D5 protein fragment containing the D5N and helicase domain",
          "short_name": "Vaccinia D5 323-785",
          "sequence": "GAMGNKLFNI AQRILDTNSV LLTERGDYIV WINNSWKFNS EEPLITKLIL SIRHQLPKEY\r\nSSELLCPRKR KTVEANIRDM LVDSVETDTY PDKLPFKNGV LDLVDGMFYS GDDAKKYTCT\r\nVSTGFKFDDT KFVEDSPEME ELMNIINDIQ PLTDENKKNR ELYEKTLSSC LCGATKGCLT\r\nFFFGETATGK STTKRLLKSA IGDLFVETGQ TILTDVLDKG PNPFIANMHL KRSVFCSELP  \r\nDFACSGSKKI RSDNIKKLTE PCVIGRPCFS NKINNRNHAT IIIDTNYKPV FDRIDNALMR\r\nRIAVVRFRTH FSQPSGREAA ENNDAYDKVK LLDEGLDGKI QNNRYRFAFL YLLVKWYKKY\r\nHVPIMKLYPT PEEIPDFAFY LKIGTLLVSS SVKHIPLMTD LSKKGYILYD NVVTLPLTTF\r\nQQKISKYFNS RLFGHDIESF INRHKKFANV SDEYLQYIFI EDISSP ",
          "organism": "Vaccinia virus",
          "uniprot_code": "P21010",
          "uniprot_range_first": 323,
          "uniprot_range_last": 785,
          "oligomerization": "hexamer",
          "molecular_type": "protein",
          "uniprot_sequence": "MDAAIRGNDVIFVLKTIGVPSACRQNEDPRFVEAFKCDELKRYIDNNPECTLFESLRDEE\nAYSIVRIFMDVDLDACLDEIDYLTAIQDFIIEVSNCVARFAFTECGAIHENVIKSMRSNF\nSLTKSTNRDKTSFHIIFLDTYTTMDTLIAMKRTLLELSRSSENPLTRSIDTAVYRRKTTL\nRVVGTRKNPNCDTIHVMQPPHDNIEDYLFTYVDMNNNSYYFSLQRRLEDLVPDKLWEPGF\nISFEDAIKRVSKIFINSIINFNDLDENNFTTVPLVIDYVTPCALCKKRSHKHPHQLSLEN\nGAIRIYKTGNPHSCKVKIVPLDGNKLFNIAQRILDTNSVLLTERGDYIVWINNSWKFNSE\nEPLITKLILSIRHQLPKEYSSELLCPRKRKTVEANIRDMLVDSVETDTYPDKLPFKNGVL\nDLVDGMFYSGDDAKKYTCTVSTGFKFDDTKFVEDSPEMEELMNIINDIQPLTDENKKNRE\nLYEKTLSSCLCGATKGCLTFFFGETATGKSTTKRLLKSAIGDLFVETGQTILTDVLDKGP\nNPFIANMHLKRSVFCSELPDFACSGSKKIRSDNIKKLTEPCVIGRPCFSNKINNRNHATI\nIIDTNYKPVFDRIDNALMRRIAVVRFRTHFSQPSGREAAENNDAYDKVKLLDEGLDGKIQ\nNNRYRFAFLYLLVKWYKKYHVPIMKLYPTPEEIPDFAFYLKIGTLLVSSSVKHIPLMTDL\nSKKGYILYDNVVTLPLTTFQQKISKYFNSRLFGHDIESFINRHKKFANVSDEYLQYIFIE\nDISSP",
          "mw": 53.48,
          "total_mw": 320.879,
          "number_molecules": 6,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
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      ],
      "buffer": {
        "name": "20 mM Tris 150 mM NaCL 5% glycerol 1mM DTT",
        "concentration_unit": "mM",
        "comment": null,
        "additive": "150 mM NaCL, 5% glycerol, 1mM DTT",
        "concentration": 20.0,
        "pka": null,
        "ph": 7.0,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Vaccinia primase D5 protein fragment containing the D5N and helicase domain",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [],
        "contributor_name": "Stephanie",
        "contributor_surname": "Hutin",
        "orcid": null
      }
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    "concentration_method": null,
    "concentration_unit": "mg/ml",
    "date": "2014-09-26",
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    "exposure_time": 2.0,
    "number_of_frames": 2000,
    "wavelength": 0.93,
    "sample_detector_distance": 2.43,
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          "log": null,
          "symmetry": "",
          "comment": "",
          "user": 124
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      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBU4_fit1_fit_img.png",
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      "p_value": 4e-06,
      "fit_residual_plot": "SASDBU4_fit1_fitresiduals_img.png",
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  "intensities_log_log_plot": "SASDBU4_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
  "bragg_peak": []
}
查看完整 manifest.json 原文
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