SASDFK8

GON7, the fifth subunit of human KEOPS

数据类型:SASBDB 实验数据 状态:Published 曲线类型:SEC-SAS 最后更新:2022-01-26T20:16:52.725524+01:00

The scattered intensities were displayed on an absolute scale (cm-1) using the scattering of water. SAXS data were normalized to the intensity of the incident beam, averaged and background subtracted using the program US-SOMO. Frames were examined individually and 30 identical frames were averaged and further processed. The corresponding SEC-elution concentration was approximately 1.5 mg/mL.

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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · GON7, the fifth subunit of human KEOPS

浓度— – 6.7 缓冲液 / pH20 mM MES, 200 mM NaCl, 5 mM β-mercaptoethanol / 6.5
实验温度15.0 设备 / 束线SOLEIL / SWING
波长0.1 nm曝光1.0 s × 255

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
EKC/KEOPS complex subunit GON7
查看序列
MGHHHHHHENLYFQGELLGEYVGQEGKPQKLRVSCEAPGDGDPFQGLLSGVAQMKDMVTELFDPLVQGEVQHRVAAAPDEDLDGDDEDDAEDENNIDNRTNFDGPSAKRPKTPS
proteinHomo sapiensQ9BXV92–100monomer分子数 112.59 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
1874[3]0.00958007320091–0.500271777004 1/A含误差列缺失 00sasbdb/entries/k8/sasdfk8/source/SASDFK8.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)12.5—Å
i0Guinier0.019714e-051/cm
i0P(r)0.01988—1/cm
mwExperimental14.7—kDa
mwGuinier I(0)14.7—kDa
mwPorod29.0—kDa
porod_volumePorod46.0—ų
rgGuinier3.080.01Å
rgP(r)3.25—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

该条目没有来源拟合记录。

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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 MES, 200 mM NaCl, 5 mM β-mercaptoethanol缓冲液浓度—
pH6.5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2017-03-26储存 / 测量温度— / 15.0
曝光时间1.0帧数255
波长0.1样品-探测器距离1.8
光源X-ray synchrotron探测器AVIEX PCCD170170
机构 / 束线SOLEIL / SWING · Saint-Aubin, France
q 范围0.096 – 5.003样品体积 / 流速65.0 / 0.3

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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curve:来源记录
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full_entry_zip:来源记录与 ZIP 内部目录(2 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:134 个字段值
字段路径原始值
codeSASDFK8
statusPublished
type_of_curveSEC-SAS
angular_unit1/A
project.titleDefects in t<sup>6</sup>A tRNA modification due to GON7 and YRDC mutations lead to Galloway-Mowat syndrome.
project.publication.titleDefects in t<sup>6</sup>A tRNA modification due to GON7 and YRDC mutations lead to Galloway-Mowat syndrome.
project.publication.author_listArrondel C, Missoury S, Snoek R, Patat J, Menara G, Collinet B, Liger D, Durand D, Gribouval O, Boyer O, Buscara L, Martin G, Machuca E, Nevo F, Lescop E, Braun DA, Boschat AC, Sanquer S, Guerrera IC, Revy P, Parisot M, Masson C, Boddaert N, Charbit M, Decramer S, Novo R, Macher MA, Ranchin B, Bacchetta J, Laurent A, Collardeau-Frachon S, van Eerde AM, Hildebrandt F, Magen D, Antignac C, van Tilbeurgh H, Mollet G
project.publication.journalNat Commun
project.publication.doi10.1038/s41467-019-11951-x
project.publication.pmid31481669
project.publication.published_date2019 Sep 3
project.statusreleased
project.submitted_date2019-07-05
project.released_date2019-09-05
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experiment.instrument.detector.typeCCD
experiment.instrument.detector.nameAVIEX PCCD170170
experiment.instrument.detector.resolutionnull
experiment.instrument.nameSOLEIL
experiment.instrument.citySaint-Aubin
experiment.instrument.countryFrance
experiment.instrument.beamline_nameSWING
experiment.instrument.beam_geometry
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourcenull
experiment.instrument.line_collimationnull
experiment.instrument.sample_path_lengthnull
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experiment.instrument.line_collimation_integrationwidthnull
experiment.instrument.xray_energynull
experiment.instrument.beam_profile_ahnull
experiment.instrument.beam_profile_alnull
experiment.sample.molecule[0].long_nameEKC/KEOPS complex subunit GON7
experiment.sample.molecule[0].short_nameGON7
experiment.sample.molecule[0].sequenceMGHHHHHHENLYFQGELLGEYVGQEGKPQKLRVSCEAPGDGDPFQGLLSGVAQMKDMVTELFDPLVQGEVQHRVAAAPDEDLDGDDEDDAEDENNIDNRTNFDGPSAKRPKTPS
experiment.sample.molecule[0].organismHomo sapiens
experiment.sample.molecule[0].uniprot_codeQ9BXV9
experiment.sample.molecule[0].uniprot_range_first2
experiment.sample.molecule[0].uniprot_range_last100
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMELLGEYVGQEGKPQKLRVSCEAPGDGDPFQGLLSGVAQMKDMVTELFDPLVQGEVQHRV AAAPDEDLDGDDEDDAEDENNIDNRTNFDGPSAKRPKTPS
experiment.sample.molecule[0].mw12.59
experiment.sample.molecule[0].total_mw12.59
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_descriptionnull
experiment.sample.buffer.name20 mM MES, 200 mM NaCl, 5 mM β-mercaptoethanol
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph6.5
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameGON7, the fifth subunit of human KEOPS
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].addressParis, France
experiment.contributor[0].affiliation[0].full_nameI2BC-CNRS
experiment.contributor[0].affiliation[0].webpagehttp://www.i2bc.paris-saclay.fr
experiment.contributor[0].contributor_namesophia
experiment.contributor[0].contributor_surnamemissoury
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2017-03-26
experiment.storage_temperaturenull
experiment.cell_temperature15.0
experiment.exposure_time1.0
experiment.number_of_frames255
experiment.wavelength0.1
experiment.sample_detector_distance1.8
experiment.concentration_minnull
experiment.concentration_max6.7
experiment.sample_volume65.0
experiment.flow_rate0.3
experiment.s_min0.096
experiment.s_max5.003
experiment.total_exposure_timenull
experiment.seccolumn10
fits[]
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionThe scattered intensities were displayed on an absolute scale (cm-1) using the scattering of water. SAXS data were normalized to the intensity of the incident beam, averaged and background subtracted using the program US-SOMO. Frames were examined individually and 30 identical frames were averaged and further processed. The corresponding SEC-elution concentration was approximately 1.5 mg/mL.
experiment_descriptionSynchrotron SAXS data from solutions of GON7 in 20 mM MES, 200 mM NaCl, 5 mM β-mercaptoethanol, pH 6.5 were collected on the SWING beam line at SOLEIL (Saint-Aubin, France) using a AVIEX PCCD170170 detector at a sample-detector distance of 1.8 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 65.00 μl sample at 6.7 mg/ml was injected at a 0.30 ml/min flow rate onto a Agilent Bio SEC-3, 300 Å column at 15°C. 255 successive 1 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.
tags[0]idp
intensity_unit1/cm
experimental_mw14.7
experimental_mw_errornull
guinier_i0_mw14.7
guinier_i0_mw_errornull
porod_mw29.0
porod_mw_errornull
pddf_i00.01988
pddf_i0_errornull
guinier_i00.01971
guinier_i0_error4e-05
pddf_rg3.25
pddf_rg_errornull
guinier_rg3.08
guinier_rg_error0.01
pddf_dmax12.5
pddf_dmax_errornull
porod_volume46.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first5
guinier_point_last47
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDFK8_datloglog_img.png
symmetrynull
last_modified2022-01-26T20:16:52.725524+01:00
bragg_peak[]
manifest.json:36 个字段值
字段路径原始值
codeSASDFK8
statussuccess
started_at2026-08-11T15:55:03.504045+00:00
finished_at2026-08-11T15:55:11.238408+00:00
source_last_modified2022-01-26T20:16:52.725524+01:00
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查看完整 summary.json 原文
{
  "code": "SASDFK8",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/A",
  "project": {
    "title": "Defects in t<sup>6</sup>A tRNA modification due to GON7 and YRDC mutations lead to Galloway-Mowat syndrome.",
    "publication": {
      "title": "Defects in t<sup>6</sup>A tRNA modification due to GON7 and YRDC mutations lead to Galloway-Mowat syndrome.",
      "author_list": "Arrondel C, Missoury S, Snoek R, Patat J, Menara G, Collinet B, Liger D, Durand D, Gribouval O, Boyer O, Buscara L, Martin G, Machuca E, Nevo F, Lescop E, Braun DA, Boschat AC, Sanquer S, Guerrera IC, Revy P, Parisot M, Masson C, Boddaert N, Charbit M, Decramer S, Novo R, Macher MA, Ranchin B, Bacchetta J, Laurent A, Collardeau-Frachon S, van Eerde AM, Hildebrandt F, Magen D, Antignac C, van Tilbeurgh H, Mollet G",
      "journal": "Nat Commun",
      "doi": "10.1038/s41467-019-11951-x",
      "pmid": "31481669",
      "published_date": "2019 Sep 3"
    },
    "status": "released",
    "submitted_date": "2019-07-05",
    "released_date": "2019-09-05"
  },
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    "s_max": 5.003,
    "total_exposure_time": null,
    "seccolumn": 10
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  "fits": [],
  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
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  "description": "The scattered intensities were displayed on an absolute scale (cm-1) using the scattering of water. SAXS data were normalized to the intensity of the incident beam, averaged and background subtracted using the program US-SOMO. Frames were examined individually and 30 identical frames were averaged and further processed. The corresponding SEC-elution concentration was approximately 1.5 mg/mL.",
  "experiment_description": "Synchrotron SAXS data from solutions of GON7 in 20 mM MES, 200 mM NaCl, 5 mM β-mercaptoethanol, pH 6.5 were collected on the SWING beam line at SOLEIL (Saint-Aubin, France) using a AVIEX PCCD170170 detector at a sample-detector distance of 1.8 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 65.00 μl sample at 6.7 mg/ml was injected at a 0.30 ml/min flow rate onto a Agilent Bio SEC-3, 300 Å column at 15°C. 255 successive 1 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.",
  "tags": [
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  "intensity_unit": "1/cm",
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  "experimental_mw_error": null,
  "guinier_i0_mw": 14.7,
  "guinier_i0_mw_error": null,
  "porod_mw": 29.0,
  "porod_mw_error": null,
  "pddf_i0": 0.01988,
  "pddf_i0_error": null,
  "guinier_i0": 0.01971,
  "guinier_i0_error": 4e-05,
  "pddf_rg": 3.25,
  "pddf_rg_error": null,
  "guinier_rg": 3.08,
  "guinier_rg_error": 0.01,
  "pddf_dmax": 12.5,
  "pddf_dmax_error": null,
  "porod_volume": 46.0,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 5,
  "guinier_point_last": 47,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDFK8_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2022-01-26T20:16:52.725524+01:00",
  "bragg_peak": []
}
查看完整 manifest.json 原文
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