SASDE98

Solution structure of Diadenylate cyclase (DacA) from Staphylococcus aureus

数据类型:SASBDB 实验数据 状态:Published 曲线类型:SEC-SAS 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 · Solution structure of Diadenylate cyclase (DacA) from Staphylococcus aureus

浓度— – — 缓冲液 / pH30 mM Tris, 150 mM NaCl / 7.5
实验温度20.0 设备 / 束线Diamond Light Source / B21
波长0.1 nm曝光3.0 s × —

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
Diadenylate cyclase
查看序列
>DACAGSHMASFLKRYTSNTYSKDEEKLIQSVSKAVQYMAKRRIGALIVFEKETGLQDYIETGIAMDSNISQELLINVFIPNTPLHDGAMIIQGTKIAAAASYLPLSDSPKISKSLGTRHRAAVGISEVSDAFTVIVSEETGDISVTFDGKLRRDISNEIFEELLAEHWFGTRFQKKGVK
proteinStaphylococcus aureusA0A0H2XIU4100–269dimer分子数 219.374 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
11365[4]0.00861189–0.314436 1/A含误差列缺失 01sasbdb/entries/98/sasde98/source/SASDE98.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)8.57—Å
i0Guinier0.031433e-05arbitrary
i0P(r)0.03133—arbitrary
mwExperimental40.2—kDa
mwPorod37.0—kDa
porod_volumePorod57.0—ų
rgGuinier2.630.04Å
rgP(r)2.63—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30 mM Tris, 150 mM NaCl缓冲液浓度—
pH7.5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2018-05-07储存 / 测量温度20.0 / 20.0
曝光时间3.0帧数—
波长0.1样品-探测器距离4.014
光源X-ray synchrotron探测器Pilatus 2M
机构 / 束线Diamond Light Source / B21 · Didcot, UK
q 范围0.086 – 3.144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(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:156 个字段值
字段路径原始值
codeSASDE98
statusPublished
type_of_curveSEC-SAS
angular_unit1/A
project.titleInhibition of the Staphylococcus aureus c-di-AMP cyclase DacA by direct interaction with the phosphoglucosamine mutase GlmM.
project.publication.titleInhibition of the Staphylococcus aureus c-di-AMP cyclase DacA by direct interaction with the phosphoglucosamine mutase GlmM.
project.publication.author_listTosi T, Hoshiga F, Millership C, Singh R, Eldrid C, Patin D, Mengin-Lecreulx D, Thalassinos K, Freemont P, Gründling A
project.publication.journalPLoS Pathog
project.publication.doi10.1371/journal.ppat.1007537
project.publication.pmid30668586
project.publication.published_date2019 Jan 22
project.statusreleased
project.submitted_date2018-11-17
project.released_date2019-01-28
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experiment.instrument.detector.resolutionnull
experiment.instrument.nameDiamond Light Source
experiment.instrument.cityDidcot
experiment.instrument.countryUK
experiment.instrument.beamline_nameB21
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experiment.instrument.type_of_sourceX-ray synchrotron
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experiment.sample.molecule[0].long_nameDiadenylate cyclase
experiment.sample.molecule[0].short_nameDacA
experiment.sample.molecule[0].sequence>DacA GSHMASFLKRYTSNTYSKDEEKLIQSVSKAVQYMAKRRIGALIVFEKETGLQDYIETGIAMDSNISQELLINVFIPNTPLHDGAMIIQGTKIAAAASYLPLSDSPKISKSLGTRHRAAVGISEVSDAFTVIVSEETGDISVTFDGKLRRDISNEIFEELLAEHWFGTRFQKKGVK
experiment.sample.molecule[0].organismStaphylococcus aureus
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experiment.sample.molecule[0].total_mw38.748
experiment.sample.molecule[0].number_molecules2
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.name30 mM Tris, 150 mM NaCl
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.5
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameSolution structure of Diadenylate cyclase (DacA) from Staphylococcus aureus
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].addressLondon, UK
experiment.contributor[0].affiliation[0].full_nameImperial College London
experiment.contributor[0].affiliation[0].webpagehttps://www.imperial.ac.uk/
experiment.contributor[0].contributor_nameTommaso
experiment.contributor[0].contributor_surnameTosi
experiment.contributor[0].orcidhttps://orcid.org/0000-0002-4564-7807
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2018-05-07
experiment.storage_temperature20.0
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experiment.total_exposure_timenull
experiment.seccolumnnull
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pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of the DacA in 30 mM Tris, 150 mM NaCl, pH 7.5 were collected using size-exclusion chromatography SAXS (SEC-SAXS) on the B21 beam line at the Diamond Light Source (Oxfordshire, UK) using a Pilatus 2M detector at a sample-to-detector distance of 4.014 m and X-ray wavelength of λ = 0.1 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). SEC-SAXS was performed at 20°C using the following parameters: Column: Superdex 200 5/150 (GE Healthcare); Flow rate: 0.075 mL/min; Sample injection concentration: 12.0 mg/mL; Injection volume: 45 μL. The data obtained through the sample elution peak (collected as consecutive 3 s exposures) were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the individual subtracted data sets were scaled and averaged to generate the scattering profile displayed in this entry.
tags[]
intensity_unitarbitrary
experimental_mw40.2
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw37.0
porod_mw_errornull
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guinier_i0_error3e-05
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pddf_rg_errornull
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pddf_dmax_errornull
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estimated_volume_errornull
guinier_point_first1
guinier_point_last183
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDE98_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
codeSASDE98
statussuccess
started_at2026-08-11T15:48:16.387687+00:00
finished_at2026-08-11T15:48:29.539545+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": "SASDE98",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/A",
  "project": {
    "title": "Inhibition of the Staphylococcus aureus c-di-AMP cyclase DacA by direct interaction with the phosphoglucosamine mutase GlmM.",
    "publication": {
      "title": "Inhibition of the Staphylococcus aureus c-di-AMP cyclase DacA by direct interaction with the phosphoglucosamine mutase GlmM.",
      "author_list": "Tosi T, Hoshiga F, Millership C, Singh R, Eldrid C, Patin D, Mengin-Lecreulx D, Thalassinos K, Freemont P, Gründling A",
      "journal": "PLoS Pathog",
      "doi": "10.1371/journal.ppat.1007537",
      "pmid": "30668586",
      "published_date": "2019 Jan 22"
    },
    "status": "released",
    "submitted_date": "2018-11-17",
    "released_date": "2019-01-28"
  },
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    "sample": {
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          "long_name": "Diadenylate cyclase",
          "short_name": "DacA",
          "sequence": ">DacA\r\nGSHMASFLKRYTSNTYSKDEEKLIQSVSKAVQYMAKRRIGALIVFEKETGLQDYIETGIAMDSNISQELLINVFIPNTPLHDGAMIIQGTKIAAAASYLPLSDSPKISKSLGTRHRAAVGISEVSDAFTVIVSEETGDISVTFDGKLRRDISNEIFEELLAEHWFGTRFQKKGVK",
          "organism": "Staphylococcus aureus",
          "uniprot_code": "A0A0H2XIU4",
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          "number_molecules": 2,
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          "molecule_description": null
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        "comment": null,
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        "pka": null,
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        "deuteration": null
      },
      "purity_method": null,
      "name": "Solution structure of Diadenylate cyclase (DacA) from Staphylococcus aureus",
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}
查看完整 manifest.json 原文
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