SASDFD5

Tetracycline repressor (class D), TetR(D)

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Merged 最后更新:2023-06-21T07:56:39.492710+02:00
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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Tetracycline repressor (class D), TetR(D)

浓度1.31 – 2.88 缓冲液 / pH50 mM Tris/HCl 150 mM NaCl 10 mM MgCl2 / 8.0
实验温度10.0 设备 / 束线PETRA III / EMBL P12
波长0.124 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
Tetracycline repressor (class D)
查看序列
SRLNRESVIDAALELLNETGIDGLTTRKLAQKLGIEQPTLYWHVKNKRALLDALAVEILARHHDYSLPAAGESWQSFLRNNAMSFRRALLRYRDGAKVHLGTRPDEKQYDTVETQLRFMTENGFSLRDGLYAISAVSHFTLGAVLEQQEHTAALTDRPAAPDENLPPLLREALQIMDSDDGEQAFLHGLESLIRGFEVQLTALLQIV
proteinEscherichia coliP0ACT42–208dimer分子数 223.259 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
11681[3]0.0385821–4.45777 1/nm含误差列缺失 0106sasbdb/entries/d5/sasdfd5/source/SASDFD5.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)7.73—nm
i0Guinier7468.9515.06arbitrary
i0P(r)7338.0—arbitrary
mwExperimental41.5—kDa
mwGuinier I(0)41.5—kDa
mwPorod52.9—kDa
porod_volumePorod84.59—nm³
rgGuinier2.640.12nm
rgP(r)2.545—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50 mM Tris/HCl 150 mM NaCl 10 mM MgCl2缓冲液浓度—
pH8.0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2013-09-23储存 / 测量温度— / 10.0
曝光时间0.05帧数20
波长0.124样品-探测器距离3.1
光源X-ray synchrotron探测器Pilatus 2M
机构 / 束线PETRA III / EMBL P12 · DESY; Hamburg, Germany
q 范围0.039 – 4.458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:159 个字段值
字段路径原始值
codeSASDFD5
statusPublished
type_of_curveMerged
angular_unit1/nm
project.titleThermodynamics, cooperativity and stability of the tetracycline repressor (TetR) upon tetracycline binding.
project.publication.titleThermodynamics, cooperativity and stability of the tetracycline repressor (TetR) upon tetracycline binding.
project.publication.author_listPalm GJ, Buchholz I, Werten S, Girbardt B, Berndt L, Delcea M, Hinrichs W
project.publication.journalBiochim Biophys Acta Proteins Proteom
project.publication.doi10.1016/j.bbapap.2020.140404
project.publication.pmid32114262
project.publication.published_date2020 Feb 27
project.statusreleased
project.submitted_date2019-04-11
project.released_date2020-03-05
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experiment.instrument.detector.resolutionnull
experiment.instrument.namePETRA III
experiment.instrument.cityDESY; Hamburg
experiment.instrument.countryGermany
experiment.instrument.beamline_nameEMBL P12
experiment.instrument.beam_geometrynull
experiment.instrument.type_of_sourceX-ray synchrotron
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experiment.instrument.xray_energynull
experiment.instrument.beam_profile_ahnull
experiment.instrument.beam_profile_alnull
experiment.sample.molecule[0].long_nameTetracycline repressor (class D)
experiment.sample.molecule[0].short_nameTetR(D)
experiment.sample.molecule[0].sequenceSRLNRESVIDAALELLNETGIDGLTTRKLAQKLGIEQPTLYWHVKNKRALLDALAVEILARHHDYSLPAAGESWQSFLRNNAMSFRRALLRYRDGAKVHLGTRPDEKQYDTVETQLRFMTENGFSLRDGLYAISAVSHFTLGAVLEQQEHTAALTDRPAAPDENLPPLLREALQIMDSDDGEQAFLHGLESLIRGFEVQLTALLQIV
experiment.sample.molecule[0].organismEscherichia coli
experiment.sample.molecule[0].uniprot_codeP0ACT4
experiment.sample.molecule[0].uniprot_range_first2
experiment.sample.molecule[0].uniprot_range_last208
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
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experiment.sample.molecule[0].mw23.259
experiment.sample.molecule[0].total_mw46.518
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.name50 mM Tris/HCl 150 mM NaCl 10 mM MgCl2
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph8.0
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameTetracycline repressor (class D), TetR(D)
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].addressInnsbruck, Austria
experiment.contributor[0].affiliation[0].full_nameMedical University of Innsbruck
experiment.contributor[0].affiliation[0].webpagehttps://www.i-med.ac.at/
experiment.contributor[0].contributor_nameSebastiaan
experiment.contributor[0].contributor_surnameWerten
experiment.contributor[0].orcidhttps://orcid.org/0000-0003-2244-9688
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2013-09-23
experiment.storage_temperaturenull
experiment.cell_temperature10.0
experiment.exposure_time0.05
experiment.number_of_frames20
experiment.wavelength0.124
experiment.sample_detector_distance3.1
experiment.concentration_min1.31
experiment.concentration_max2.88
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.039
experiment.s_max4.458
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].softwarePDB (Protein Data Bank)
fits[0].models[0].pdb_link[0].pdb_code4v2f
fits[0].models[0].pdb_link[0].ext_code4V2F
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fits[0].models[0].model_mw43.66
fits[0].models[0].bead_radiusnull
fits[0].models[0].lognull
fits[0].models[0].symmetryp2
fits[0].models[0].commentA dimer was generated from the PDB entry by applying crystallographic symmetry
fits[0].models[0].user438
fits[0].fit_unit1/A
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fits[0].softwareCRYSOL
fits[0].chi_square_value1.545
fits[0].p_value0.0
fits[0].fit_residual_plotSASDFD5_fit1_fitresiduals_img.png
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fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of TetR(D) in 50 mM Tris/HCl 150 mM NaCl 10 mM MgCl2, pH 8 were collected on the EMBL P12 beam line at PETRA III (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3.1 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1.3 and 2.9 mg/ml were measured at 10°C. 20 successive 0.050 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. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.
tags[]
intensity_unitarbitrary
experimental_mw41.5
experimental_mw_errornull
guinier_i0_mw41.5
guinier_i0_mw_errornull
porod_mw52.9
porod_mw_errornull
pddf_i07338.0
pddf_i0_errornull
guinier_i07468.95
guinier_i0_error15.06
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pddf_rg_errornull
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guinier_rg_error0.12
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pddf_dmax_errornull
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porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first28
guinier_point_last172
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDFD5_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
codeSASDFD5
statussuccess
started_at2026-08-11T14:45:33.668157+00:00
finished_at2026-08-11T14:45:43.390411+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": "SASDFD5",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/nm",
  "project": {
    "title": "Thermodynamics, cooperativity and stability of the tetracycline repressor (TetR) upon tetracycline binding.",
    "publication": {
      "title": "Thermodynamics, cooperativity and stability of the tetracycline repressor (TetR) upon tetracycline binding.",
      "author_list": "Palm GJ, Buchholz I, Werten S, Girbardt B, Berndt L, Delcea M, Hinrichs W",
      "journal": "Biochim Biophys Acta Proteins Proteom",
      "doi": "10.1016/j.bbapap.2020.140404",
      "pmid": "32114262",
      "published_date": "2020 Feb 27"
    },
    "status": "released",
    "submitted_date": "2019-04-11",
    "released_date": "2020-03-05"
  },
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查看完整 manifest.json 原文
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