SASDEA3

Labeled thioredoxin (TRX-Alexa488/Alexa594) with denaturant

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Single concentration 最后更新:2023-06-21T07:56:39.492710+02:00

The protein contains a penultimate non-canonical amino acid p-acetylphenylalanine (207 Da) that is represented as U (selenocysteine, 168 Da) in the amino acid sequence for the entry. Therefore, the calculated MW from sequence (MW(expected)) must be adjusted accordingly (ca. 40 Da).

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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Labeled thioredoxin (TRX-Alexa488/Alexa594) with denaturant

浓度— – 10.0 缓冲液 / pHPBS, 10 mM DTT, 6 M urea, 0.3 M KCl / 7.4
实验温度23.0 设备 / 束线PETRA III / EMBL P12
波长0.1 nm曝光0.05 s × 20

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
Thioredoxin 1
查看序列
>U=P-ACETYLPHENYLALANINE.CWASLABELEDWITHALEXAFLUOR594C5MALEIMIDE.UWASLABELEDWITHALEXAFLUOR488C5HYDROXYLAMINEGCDKIIHLTDDSFDTDVLKADGAILVDFWAEWSGPSKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANUA
proteinEscherichia coliP0AA252–106monomer分子数 111.753 kDa
Alexa Fluor™ 594 C5 Maleimideother———–—monomer分子数 10.886 kDa
Alexa Fluor™ 488 C5 Hydroxylamineother———–—monomer分子数 10.7 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
11714[3]0.0767596–4.58324 1/nm含误差列缺失 04sasbdb/entries/a3/sasdea3/source/SASDEA3.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)13.88—nm
i0Guinier315.41.6arbitrary
i0P(r)320.71.7arbitrary
mwExperimental9.5—kDa
porod_volumePorod30.9—nm³
rgGuinier3.20.08nm
rgP(r)3.4660.05nm

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PBS, 10 mM DTT, 6 M urea, 0.3 M KCl缓冲液浓度—
pH7.4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2013-06-15储存 / 测量温度— / 23.0
曝光时间0.05帧数20
波长0.1样品-探测器距离3.0
光源X-ray synchrotron探测器Pilatus 2M
机构 / 束线PETRA III / EMBL P12 · DESY; Hamburg, Germany
q 范围0.077 – 4.583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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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:168 个字段值
字段路径原始值
codeSASDEA3
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleDecoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements.
project.publication.titleDecoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements.
project.publication.author_listFuertes G, Banterle N, Ruff KM, Chowdhury A, Mercadante D, Koehler C, Kachala M, Estrada Girona G, Milles S, Mishra A, Onck PR, Gräter F, Esteban-Martín S, Pappu RV, Svergun DI, Lemke EA
project.publication.journalProc Natl Acad Sci U S A
project.publication.doi10.1073/pnas.1704692114
project.publication.pmid28716919
project.publication.published_date2017 Aug 1
project.statusreleased
project.submitted_date2018-08-16
project.released_date2018-08-18
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experiment.instrument.cityDESY; Hamburg
experiment.instrument.countryGermany
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experiment.sample.molecule[0].long_nameThioredoxin 1
experiment.sample.molecule[0].short_nameTRX-488/594
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experiment.sample.molecule[0].uniprot_codeP0AA25
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experiment.sample.molecule[1].short_nameAlexa594
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experiment.sample.molecule[1].organismnull
experiment.sample.molecule[1].uniprot_codenull
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experiment.sample.molecule[2].molecule_descriptionnull
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experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.4
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameLabeled thioredoxin (TRX-Alexa488/Alexa594) with denaturant
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].addressPrague, Czech Republic
experiment.contributor[0].affiliation[0].full_nameInstitute of Biotechnology CAS v.v.i.
experiment.contributor[0].affiliation[0].webpagehttp://www.ibt.cas.cz/
experiment.contributor[0].contributor_nameGustavo
experiment.contributor[0].contributor_surnameFuertes Vives
experiment.contributor[0].orcidhttps://orcid.org/0000-0002-8564-8644
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2013-06-15
experiment.storage_temperaturenull
experiment.cell_temperature23.0
experiment.exposure_time0.05
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experiment.seccolumnnull
fits[]
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionThe protein contains a penultimate non-canonical amino acid p-acetylphenylalanine (207 Da) that is represented as U (selenocysteine, 168 Da) in the amino acid sequence for the entry. Therefore, the calculated MW from sequence (MW(expected)) must be adjusted accordingly (ca. 40 Da).
experiment_descriptionnull
tags[0]idp
intensity_unitarbitrary
experimental_mw9.5
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i0320.7
pddf_i0_error1.7
guinier_i0315.4
guinier_i0_error1.6
pddf_rg3.466
pddf_rg_error0.05
guinier_rg3.2
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pddf_dmax_errornull
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porod_volume_errornull
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estimated_volume_errornull
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guinier_point_last126
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDEA3_datloglog_img.png
symmetrynull
last_modified2023-06-21T07:56:39.492710+02:00
bragg_peak[]
manifest.json:36 个字段值
字段路径原始值
codeSASDEA3
statussuccess
started_at2026-08-11T13:55:59.155789+00:00
finished_at2026-08-11T13:56:07.600535+00:00
source_last_modified2023-06-21T07:56:39.492710+02:00
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查看完整 summary.json 原文
{
  "code": "SASDEA3",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements.",
    "publication": {
      "title": "Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements.",
      "author_list": "Fuertes G, Banterle N, Ruff KM, Chowdhury A, Mercadante D, Koehler C, Kachala M, Estrada Girona G, Milles S, Mishra A, Onck PR, Gräter F, Esteban-Martín S, Pappu RV, Svergun DI, Lemke EA",
      "journal": "Proc Natl Acad Sci U S A",
      "doi": "10.1073/pnas.1704692114",
      "pmid": "28716919",
      "published_date": "2017 Aug 1"
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          "long_name": "Alexa Fluor™ 488 C5 Hydroxylamine",
          "short_name": "Alexa488",
          "sequence": null,
          "organism": null,
          "uniprot_code": null,
          "uniprot_range_first": null,
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        "name": "PBS, 10 mM DTT, 6 M urea, 0.3 M KCl",
        "concentration_unit": null,
        "comment": null,
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    "contributor": [
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        "affiliation": [
          {
            "short_name": null,
            "address": "Prague, Czech Republic",
            "full_name": "Institute of Biotechnology CAS v.v.i.",
            "webpage": "http://www.ibt.cas.cz/"
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        "contributor_name": "Gustavo",
        "contributor_surname": "Fuertes Vives",
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    ],
    "concentration_method": null,
    "concentration_unit": null,
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  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDEA3_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2023-06-21T07:56:39.492710+02:00",
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}
查看完整 manifest.json 原文
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