SASDEN9

HcpR transcriptional regulator of Porphyromonas gingivalis

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Single concentration 最后更新:2020-08-28T15:28:14.076959+02:00
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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · HcpR transcriptional regulator of Porphyromonas gingivalis

浓度— – 2.0 缓冲液 / pH25 mM Tris 150 mM NaCl 1mM TCEP / 7.5
实验温度21.0 设备 / 束线Advanced Light Source (ALS) / 12.3.1 (SIBYLS)
波长0.103 nm曝光60.0 s × —

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
Hcp Transcriptional regulator
查看序列
MDPEFDLLLKAWKSSGLSVGMKDDELLALLESCSYRVERLKAEELYAIGGDKLQDLRIVGVGEIRAEMVGPSGKQILIDTLAVGRILAPALLFASENILPVTLFANEDSVLFRIGKEEFKGMMHKYPTLMENFIGMISDISAFLMKKIHQLSLRSLQGKIGDYLFQLYTKDGSNRIVVESSWKELSDRFGVNRQSLARSLSQLEEEGIIRVDGKSIEILQPNRLSRL
proteinPorphyromonas gingivalisQ7MVK41–227dimer分子数 225.495 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
1513[3]0.014291–0.325614 1/A含误差列缺失 00sasbdb/entries/n9/sasden9/source/SASDEN9.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)10.5—Å
i0Guinier282.90.57arbitrary
i0P(r)283.10.9arbitrary
mwExperimental44.03—kDa
mwPorod48.0—kDa
porod_volumePorod76.0—ų
rgGuinier2.890.05Å
rgP(r)2.930.01Å

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25 mM Tris 150 mM NaCl 1mM TCEP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2014-01-24储存 / 测量温度4.0 / 21.0
曝光时间60.0帧数—
波长0.103样品-探测器距离3.5
光源X-ray synchrotron探测器Pilatus3 X 2M
机构 / 束线Advanced Light Source (ALS) / 12.3.1 (SIBYLS) · Berkeley, CA, USA
q 范围0.143 – 3.256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
curvesasbdb/entries/n9/sasden9/source/SASDEN9.datdownloaded233733b0f58cf2805ba5e16ef1372c3a1f3b649db1482a45c689627f38f25e58abeaf下载查看原文件源站
full_entry_zipsasbdb/entries/n9/sasden9/source/SASDEN9.zipdownloaded196548c4b177d1ec915a9cf640b40ee14eb1051e28c5151c0923ed2a55317c2588582e下载查看原文件源站
pddfsasbdb/entries/n9/sasden9/source/SASDEN9.outdownloaded42968b0367ae4cb2b0bf986f8a9b1b93c12a659b4182a970ce45ff01c5fb57921a77f下载查看原文件源站
sascifsasbdb/entries/n9/sasden9/source/SASDEN9.sascifdownloaded109864197a8a6787c8fb0a160680142b6c356202dcffb59cc2789b1e3e4c26976b5fc89下载查看原文件源站
summarysasbdb/entries/n9/sasden9/source/summary.jsondownloaded86689e5f1b783b75a3d9b289438832381cf66b33f25f7cc14a5eed1f5fbd8b0ade59下载查看原文件源站
curve:来源记录
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full_entry_zip:来源记录与 ZIP 内部目录(7 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:182 个字段值
字段路径原始值
codeSASDEN9
statusPublished
type_of_curveSingle concentration
angular_unit1/A
project.titleNitrosative stress sensing in Porphyromonas gingivalis: structure of and heme binding by the transcriptional regulator HcpR.
project.publication.titleNitrosative stress sensing in Porphyromonas gingivalis: structure of and heme binding by the transcriptional regulator HcpR.
project.publication.author_listBelvin BR, Musayev FN, Burgner J, Scarsdale JN, Escalante CR, Lewis JP
project.publication.journalActa Crystallogr D Struct Biol
project.publication.doi10.1107/S205979831900264X
project.publication.pmid30988260
project.publication.published_date2019 Apr 1
project.statusreleased
project.submitted_date2019-01-03
project.released_date2019-04-17
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intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDEN9.dat
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experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus3 X 2M
experiment.instrument.detector.resolution172.0
experiment.instrument.nameAdvanced Light Source (ALS)
experiment.instrument.cityBerkeley, CA
experiment.instrument.countryUSA
experiment.instrument.beamline_name12.3.1 (SIBYLS)
experiment.instrument.beam_geometry
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourcenull
experiment.instrument.line_collimationnull
experiment.instrument.sample_path_lengthnull
experiment.instrument.line_collimation_slitlengthnull
experiment.instrument.line_collimation_integrationwidthnull
experiment.instrument.xray_energynull
experiment.instrument.beam_profile_ahnull
experiment.instrument.beam_profile_alnull
experiment.sample.molecule[0].long_nameHcp Transcriptional regulator
experiment.sample.molecule[0].short_nameHcpR
experiment.sample.molecule[0].sequenceMDPEFDLLLKAWKSSGLSVGMKDDELLALLESCSYRVERLKAEELYAIGGDKLQDLRIVG VGEIRAEMVGPSGKQILIDTLAVGRILAPALLFASENILPVTLFANEDSVLFRIGKEEFK GMMHKYPTLMENFIGMISDISAFLMKKIHQLSLRSLQGKIGDYLFQLYTKDGSNRIVVESSWKELSDRFG VNRQSLARSLSQLEEEGIIRVDGKSIEILQPNRLSRL
experiment.sample.molecule[0].organismPorphyromonas gingivalis
experiment.sample.molecule[0].uniprot_codeQ7MVK4
experiment.sample.molecule[0].uniprot_range_first1
experiment.sample.molecule[0].uniprot_range_last227
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMDPEFDLLLKAWKSSGLSVGMKDDELLALLESCSYRVERLKAEELYAIGGDKLQDLRIVG VGEIRAEMVGPSGKQILIDTLAVGRILAPALLFASENILPVTLFANEDSVLFRIGKEEFK GMMHKYPTLMENFIGMISDISAFLMKKIHQLSLRSLQGKIGDYLFQLYTKDGSNRIVVES SWKELSDRFGVNRQSLARSLSQLEEEGIIRVDGKSIEILQPNRLSRLE
experiment.sample.molecule[0].mw25.495
experiment.sample.molecule[0].total_mw50.99
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.name25 mM Tris 150 mM NaCl 1mM TCEP
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.nameHcpR transcriptional regulator of Porphyromonas gingivalis
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].addressRichmond, Virginia, USA
experiment.contributor[0].affiliation[0].full_nameVirginia Commonwealth University
experiment.contributor[0].affiliation[0].webpagehttps://www.vcu.edu/
experiment.contributor[0].contributor_nameBenjamin
experiment.contributor[0].contributor_surnameBelvin
experiment.contributor[0].orcid
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2014-01-24
experiment.storage_temperature4.0
experiment.cell_temperature21.0
experiment.exposure_time60.0
experiment.number_of_framesnull
experiment.wavelength0.103
experiment.sample_detector_distance3.5
experiment.concentration_minnull
experiment.concentration_max2.0
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.143
experiment.s_max3.256
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].bead_radius1.9
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fits[0].fit_unit1/A
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fits[0].softwareEOM/GAJOE
fits[0].chi_square_value0.655
fits[0].p_value0.0
fits[0].fit_residual_plotSASDEN9_fit1_fitresiduals_img.png
fits[0].fit_datahttps://www.sasbdb.org/media/fitting_files/SASDEN9_fit1.fit
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fits[0].software_versionnull
fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of Porphyromonas gingivalis HcpR in 25 mM Trish 150 mM NaCl, 2mM TCEP pH 7.5 were collected on the SIBYLS beam line at the Lawrence Berkeley National Laboratory (Berkeley, CA, USA) using a Pilatus3 X 2M detector at a sample-detector distance of 3.5 meters at a wavelength of λ = 0.103 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 2.0 mg/ml was measured at 21°C. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.
tags[]
intensity_unitarbitrary
experimental_mw44.03
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw48.0
porod_mw_errornull
pddf_i0283.1
pddf_i0_error0.9
guinier_i0282.9
guinier_i0_error0.57
pddf_rg2.93
pddf_rg_error0.01
guinier_rg2.89
guinier_rg_error0.05
pddf_dmax10.5
pddf_dmax_errornull
porod_volume76.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first15
guinier_point_last51
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDEN9_datloglog_img.png
symmetrynull
last_modified2020-08-28T15:28:14.076959+02:00
bragg_peak[]
manifest.json:36 个字段值
字段路径原始值
codeSASDEN9
statussuccess
started_at2026-08-11T16:18:22.393065+00:00
finished_at2026-08-11T16:18:36.619255+00:00
source_last_modified2020-08-28T15:28:14.076959+02:00
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查看完整 summary.json 原文
{
  "code": "SASDEN9",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/A",
  "project": {
    "title": "Nitrosative stress sensing in Porphyromonas gingivalis: structure of and heme binding by the transcriptional regulator HcpR.",
    "publication": {
      "title": "Nitrosative stress sensing in Porphyromonas gingivalis: structure of and heme binding by the transcriptional regulator HcpR.",
      "author_list": "Belvin BR, Musayev FN, Burgner J, Scarsdale JN, Escalante CR, Lewis JP",
      "journal": "Acta Crystallogr D Struct Biol",
      "doi": "10.1107/S205979831900264X",
      "pmid": "30988260",
      "published_date": "2019 Apr 1"
    },
    "status": "released",
    "submitted_date": "2019-01-03",
    "released_date": "2019-04-17"
  },
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  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEN9.dat",
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  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEN9.sascif",
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查看完整 manifest.json 原文
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