SASDBJ2

Wild-type archaeal biofilm regulator 1 (ABfR1) bound to 40bp dsDNA-Sa oligonucleotide.

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 · Wild-type archaeal biofilm regulator 1 (ABfR1) bound to 40bp dsDNA-Sa oligonucleotide.

浓度— – 3.5 mg/ml缓冲液 / pH0.5 x Tris/Borate/EDTA (TBE) / —
实验温度4.0 设备 / 束线ESRF / BM29
波长0.93 nm曝光20.0 s × 10

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
40bp long dsDNA-Sa Oligonucleotide
查看序列
GTAGTAAGATTTAAAAAAACATACTAAGATATAAATTAAC
DNA———–—monomer分子数 124.7 kDa
Wild-type archaeal biofilm regulator 1 (ABfR1: Transcriptional regulator ArsR family).
查看序列
MSIEITEKYVILKRFLSVAYGLSESEIDTFLRILESKEGKDIDAISAELKISKSRTSIILKKLSDAGLVDKEKGDNMKGGRPKYVYSVNKEELKNRLIAKSEELCKELNQVIKSFI
proteinSulfolobus acidocaldariusQ4JBH11–116dimer分子数 213.16 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
11043[3]0.0326864–4.933595 1/nm含误差列缺失 04sasbdb/entries/j2/sasdbj2/source/SASDBJ2.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)11.76—nm
i0Guinier47.93——
i0P(r)51.3——
mwExperimental51.3—kDa
mwGuinier I(0)47.93—kDa
mwPorod41.0—kDa
rgGuinier3.0—nm
rgP(r)3.35—nm

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0.5 x Tris/Borate/EDTA (TBE)缓冲液浓度0.5 v/v
pH—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2015-08-27储存 / 测量温度4.0 / 4.0
曝光时间20.0帧数10
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0.033 – 4.934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:173 个字段值
字段路径原始值
codeSASDBJ2
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleWing phosphorylation is a major functional determinant of the Lrs14-type biofilm and motility regulator AbfR1 in Sulfolobus acidocaldarius.
project.publication.titleWing phosphorylation is a major functional determinant of the Lrs14-type biofilm and motility regulator AbfR1 in Sulfolobus acidocaldarius.
project.publication.author_listLi L, Banerjee A, Bischof LF, Maklad HR, Hoffmann L, Henche AL, Veliz F, Bildl W, Schulte U, Orell A, Essen LO, Peeters E, Albers SV
project.publication.journalMol Microbiol
project.publication.doi10.1111/mmi.13735
project.publication.pmid28628237
project.publication.published_date2017 Sep
project.statusreleased
project.submitted_date2015-10-01
project.released_date2017-05-23
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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
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experiment.instrument.sample_path_lengthnull
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experiment.instrument.beam_profile_alnull
experiment.sample.molecule[0].long_name40bp long dsDNA-Sa Oligonucleotide
experiment.sample.molecule[0].short_namedsDNA-Sa Oligo
experiment.sample.molecule[0].sequenceGTAGTAAGATTTAAAAAAACATACTAAGATATAAATTAAC
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experiment.sample.molecule[0].uniprot_codenull
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experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
experiment.sample.molecule[0].molecule_descriptionnull
experiment.sample.molecule[1].long_nameWild-type archaeal biofilm regulator 1 (ABfR1: Transcriptional regulator ArsR family).
experiment.sample.molecule[1].short_nameABfR1-WT
experiment.sample.molecule[1].sequenceMSIEITEKYVILKRFLSVAYGLSESEIDTFLRILESKEGKDIDAISAELKISKSRTSIIL KKLSDAGLVDKEKGDNMKGGRPKYVYSVNKEELKNRLIAKSEELCKELNQVIKSFI
experiment.sample.molecule[1].organismSulfolobus acidocaldarius
experiment.sample.molecule[1].uniprot_codeQ4JBH1
experiment.sample.molecule[1].uniprot_range_first1
experiment.sample.molecule[1].uniprot_range_last116
experiment.sample.molecule[1].oligomerizationdimer
experiment.sample.molecule[1].molecular_typeprotein
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experiment.sample.molecule[1].mw13.16
experiment.sample.molecule[1].total_mw26.32
experiment.sample.molecule[1].number_molecules2
experiment.sample.molecule[1].complex_stateFalse
experiment.sample.molecule[1].deuterationnull
experiment.sample.molecule[1].molecule_sourcebiological
experiment.sample.molecule[1].molecule_descriptionnull
experiment.sample.buffer.name0.5 x Tris/Borate/EDTA (TBE)
experiment.sample.buffer.concentration_unitv/v
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experiment.sample.buffer.additivenull
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experiment.sample.buffer.pkanull
experiment.sample.buffer.phnull
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameWild-type archaeal biofilm regulator 1 (ABfR1) bound to 40bp dsDNA-Sa oligonucleotide.
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].addressMarburg, Germany
experiment.contributor[0].affiliation[0].full_namePhilipps-Universität Marburg
experiment.contributor[0].affiliation[0].webpage
experiment.contributor[0].contributor_nameAnkan
experiment.contributor[0].contributor_surnameBanerjee
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitmg/ml
experiment.date2015-08-27
experiment.storage_temperature4.0
experiment.cell_temperature4.0
experiment.exposure_time20.0
experiment.number_of_frames10
experiment.wavelength0.93
experiment.sample_detector_distance2.43
experiment.concentration_minnull
experiment.concentration_max3.5
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.033
experiment.s_max4.934
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].softwareDAMMIN
fits[0].models[0].pdb_link[]
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fits[0].p_value2e-06
fits[0].fit_residual_plotSASDBJ2_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 N terminal affinity tag cleaved (by thrombin) wild type AbfR1 in complex with SaOligo in 0.5 x TBE buffer was collected on the BM29 beam line on the storage ring ESRF (Grenoble, France) using a 2D Photon counting Pilatus 1M pixel detector (s = 4π sin θ/λ, where 2θ is the scattering angle). A single concentration of 3.5mg/ mL was measured in 10 successive 20 second frames. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted .The analysis was performed using the ATSAS package. The displayed model is the best fit model with the lowest reduced Chi-squared value (1.55) after imposing P2 symmetry. The DNA is considerably bent in complex with ABfR1.
tags[]
intensity_unitnull
experimental_mw51.3
experimental_mw_errornull
guinier_i0_mw47.93
guinier_i0_mw_errornull
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porod_mw_errornull
pddf_i051.3
pddf_i0_errornull
guinier_i047.93
guinier_i0_errornull
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pddf_rg_errornull
guinier_rg3.0
guinier_rg_errornull
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pddf_dmax_errornull
porod_volumenull
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first52
guinier_point_last83
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDBJ2_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
codeSASDBJ2
statussuccess
started_at2026-08-11T13:39:18.782209+00:00
finished_at2026-08-11T13:39:27.134122+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": "SASDBJ2",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Wing phosphorylation is a major functional determinant of the Lrs14-type biofilm and motility regulator AbfR1 in Sulfolobus acidocaldarius.",
    "publication": {
      "title": "Wing phosphorylation is a major functional determinant of the Lrs14-type biofilm and motility regulator AbfR1 in Sulfolobus acidocaldarius.",
      "author_list": "Li L, Banerjee A, Bischof LF, Maklad HR, Hoffmann L, Henche AL, Veliz F, Bildl W, Schulte U, Orell A, Essen LO, Peeters E, Albers SV",
      "journal": "Mol Microbiol",
      "doi": "10.1111/mmi.13735",
      "pmid": "28628237",
      "published_date": "2017 Sep"
    },
    "status": "released",
    "submitted_date": "2015-10-01",
    "released_date": "2017-05-23"
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            "address": "Marburg, Germany",
            "full_name": "Philipps-Universität Marburg",
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  "experiment_description": "X-ray synchrotron radiation scattering data from solutions of N terminal affinity tag cleaved (by thrombin) wild type AbfR1 in complex with SaOligo in 0.5 x TBE buffer was collected on the BM29 beam line on the storage ring ESRF (Grenoble, France) using a 2D Photon counting Pilatus 1M pixel detector (s = 4π sin θ/λ, where 2θ is the scattering angle). A single concentration of 3.5mg/ mL was measured in 10 successive 20 second frames. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted .The analysis was performed using the ATSAS package. The displayed model is the best fit model with the lowest reduced Chi-squared value (1.55) after imposing P2 symmetry. The DNA is considerably bent in complex with ABfR1.",
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  "last_modified": "2019-12-06T13:07:15.624532+01:00",
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}
查看完整 manifest.json 原文
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