SASDD73

Flavin reductase Pden_5119

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Merged 最后更新:2023-08-31T11:57:49.604042+02:00
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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Flavin reductase Pden_5119

浓度1.5 – 7.5 缓冲液 / pH50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole / 8.0
实验温度4.0 设备 / 束线CEITEC / Rigaku BioSAXS-1000
波长0.154 nm曝光600.0 s × 30

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
NADPH-dependent FMN reductase
查看序列
MPGPRIVAFAGSWSRPSKTRSLVEEAARRAVARFGGSAHVFDIADLGPDFGSLRQPQDGPHTRHLDAFLAADALIVASPVYKGSYTGLFKHFIDLIEPVALVGKPVLLAATGGGDRHALVIEHQLRPVFGFFEAHTLATGLYVSASDFGPDGLASEAASTRLDRAVAQFAAHLSRHDAAPLLAVGLEHHHHHH
proteinParacoccus denitrificansA1BCD5—–—dimer分子数 220.596 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
1200[3]0.0152168–0.301234 1/A含误差列缺失 02sasbdb/entries/73/sasdd73/source/SASDD73.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)6.27—Å
i0Guinier0.140.0015arbitrary
i0P(r)0.1389—arbitrary
mwExperimental41.0—kDa
mwPorod43.6—kDa
porod_volumePorod69.8—ų
rgGuinier2.340.098Å
rgP(r)2.3—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50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole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2016-02-22储存 / 测量温度4.0 / 4.0
曝光时间600.0帧数30
波长0.154样品-探测器距离0.48
光源X-ray in house探测器Pilatus 100K
机构 / 束线CEITEC / Rigaku BioSAXS-1000 · Brno, Czech Republic
q 范围0.152 – 3.012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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full_entry_zipsasbdb/entries/73/sasdd73/source/SASDD73.zipdownloaded1358931e7aea0210441a79c032e01698bcf7cc7e3db7e4c768809832928098f732e8e7下载查看原文件源站
pddfsasbdb/entries/73/sasdd73/source/SASDD73.outdownloaded2257258d006e99d928029a0c86d47211c7270eb8f0e22e57554a8cb2f6b4d319c8543下载查看原文件源站
sascifsasbdb/entries/73/sasdd73/source/SASDD73.sascifdownloaded622358b4e861e8f6267672aa97f7d47ba3ca50f195a0985bffce68a70fbfb81dcf2a89下载查看原文件源站
summarysasbdb/entries/73/sasdd73/source/summary.jsondownloaded89971f9e6aad7d9e111dcf8ea4ca5185c0db3fa29ddbaaf6e89984deb80832c818a2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(8 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
codeSASDD73
statusPublished
type_of_curveMerged
angular_unit1/A
project.titleStructural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans.
project.publication.titleStructural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans.
project.publication.author_listKryl M, Sedláček V, Kučera I
project.publication.journalInt J Mol Sci
project.publication.doi10.3390/ijms24043732
project.publication.pmid36835143
project.publication.published_date2023 Feb 13
project.statusreleased
project.submitted_date2018-01-23
project.released_date2023-08-31
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experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus 100K
experiment.instrument.detector.resolution172.0
experiment.instrument.nameCEITEC
experiment.instrument.cityBrno
experiment.instrument.countryCzech Republic
experiment.instrument.beamline_nameRigaku BioSAXS-1000
experiment.instrument.beam_geometry
experiment.instrument.type_of_sourceX-ray in house
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_nameNADPH-dependent FMN reductase
experiment.sample.molecule[0].short_namePden_5119
experiment.sample.molecule[0].sequenceMPGPRIVAFAGSWSRPSKTRSLVEEAARRAVARFGGSAHVFDIADLGPDFGSLRQPQDGP HTRHLDAFLAADALIVASPVYKGSYTGLFKHFIDLIEPVALVGKPVLLAATGGGDRHALV IEHQLRPVFGFFEAHTLATGLYVSASDFGPDGLASEAASTRLDRAVAQFAAHLSRHDAAP LLAVGLEHHHHHH
experiment.sample.molecule[0].organismParacoccus denitrificans
experiment.sample.molecule[0].uniprot_codeA1BCD5
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMPGPRIVAFAGSWSRPSKTRSLVEEAARRAVARFGGSAHVFDIADLGPDFGSLRQPQDGP HTRHLDAFLAADALIVASPVYKGSYTGLFKHFIDLIEPVALVGKPVLLAATGGGDRHALV IEHQLRPVFGFFEAHTLATGLYVSASDFGPDGLASEAASTRLDRAVAQFAAHLSRHDAAP LLAVG
experiment.sample.molecule[0].mw20.596
experiment.sample.molecule[0].total_mw41.192
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
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experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
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experiment.sample.buffer.pkanull
experiment.sample.buffer.ph8.0
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameFlavin reductase Pden_5119
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
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experiment.contributor[0].affiliation[0].webpagehttps://www.ceitec.eu/
experiment.contributor[0].contributor_nameTomas
experiment.contributor[0].contributor_surnameKlumpler
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2016-02-22
experiment.storage_temperature4.0
experiment.cell_temperature4.0
experiment.exposure_time600.0
experiment.number_of_frames30
experiment.wavelength0.154
experiment.sample_detector_distance0.48
experiment.concentration_min1.5
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experiment.flow_ratenull
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experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[1].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSAXS data from solutions of flavin reductase Pden_5119 in 50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole, pH 8, were collected on a Rigaku BioSAXS-1000 instrument at the Central European Institute of Technology, CEITEC, (Brno, Czech Republic) using a Pilatus 100K detector at a sample-detector distance of 0.5 m and at a wavelength of λ = 0.154 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1.5 and 7.5 mg/ml were measured at 4°C. 30 successive 600 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_mw41.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw43.6
porod_mw_errornull
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guinier_i00.14
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pddf_rg_errornull
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pddf_dmax_errornull
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porod_volume_errornull
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estimated_volume_errornull
guinier_point_first1
guinier_point_last29
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDD73_datloglog_img.png
symmetrynull
last_modified2023-08-31T11:57:49.604042+02:00
bragg_peak[]
manifest.json:36 个字段值
字段路径原始值
codeSASDD73
statussuccess
started_at2026-08-11T13:53:50.211184+00:00
finished_at2026-08-11T13:53:59.773558+00:00
source_last_modified2023-08-31T11:57:49.604042+02:00
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查看完整 summary.json 原文
{
  "code": "SASDD73",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/A",
  "project": {
    "title": "Structural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans.",
    "publication": {
      "title": "Structural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans.",
      "author_list": "Kryl M, Sedláček V, Kučera I",
      "journal": "Int J Mol Sci",
      "doi": "10.3390/ijms24043732",
      "pmid": "36835143",
      "published_date": "2023 Feb 13"
    },
    "status": "released",
    "submitted_date": "2018-01-23",
    "released_date": "2023-08-31"
  },
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查看完整 manifest.json 原文
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