SASDBZ2

Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Single concentration 最后更新:2023-06-21T07:56:39.492710+02:00

The models displayed above are, from top to bottom: 1) An individual DAMMIN dummy atom model and; 2) CORAL rigid body model with the associated CRYSOL fit to the data. All of the individual DAMMIN models and associated fits can be found in the zip archive for this entry along with the CORAL modelling results.

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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli

浓度1.4 – 10.8 缓冲液 / pH50 mM Tris 10 mM NaCl / 7.5
实验温度10.0 设备 / 束线PETRA III / EMBL P12
波长0.12 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
Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli
查看序列
MTDIAQLLGKDADNLLQHCCMTIPSDQLYLPGHDYVDRVMIDNNRPPAVLRNMQTLYNTGRLAGTGYLSILPVDQGVEHSAGASFAANPLYFDPKNIVELAIEAGCNCVASTYGVLASVSRRYAHRIPFLVKLNHNETLSYPNTYDQTLYASVEQAFNMGAVAVGATIYFGSEESRRQIEEISAAFERAHELGMVTVLWAYLRNSAFKKDGVDYHVSADLTGQANHLAATIGADIVKQKMAENNGGYKAINYGYTDDRVYSKLTSENPIDLVRYQLANCYMGRAGLINSGGAAGGETDLSDAVRTAVINKRAGGMGLILGRKAFKKSMADGVKLINAVQDVYLDSKITIA
proteinEscherichia coliA0A0K4BP99—–—decamer分子数 1038.056 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
11198[3]0.0846518–3.23367 1/nm含误差列缺失 011sasbdb/entries/z2/sasdbz2/source/SASDBZ2.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)12.73—nm
i0Guinier16826.025.0—
i0P(r)16670.018.0—
mwExperimental340.0—kDa
mwGuinier I(0)340.0—kDa
mwPorod302.0—kDa
porod_volumePorod484.0—nm³
rgGuinier4.430.02nm
rgP(r)4.340.04nm

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 10 mM NaCl缓冲液浓度50.0 mM
pH7.5添加剂10 mM NaCl
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2013-06-30储存 / 测量温度10.0 / 10.0
曝光时间0.05帧数20
波长0.12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0.085 – 3.234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(9 项)
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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:179 个字段值
字段路径原始值
codeSASDBZ2
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleX-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism.
project.publication.titleX-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism.
project.publication.author_listDadinova LA, Shtykova EV, Konarev PV, Rodina EV, Snalina NE, Vorobyeva NN, Kurilova SA, Nazarova TI, Jeffries CM, Svergun DI
project.publication.journalPLoS One
project.publication.doi10.1371/journal.pone.0156105
project.publication.pmid27227414
project.publication.published_date2016
project.statusreleased
project.submitted_date2015-12-14
project.released_date2016-07-01
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sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDBZ2.sascif
experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus 2M
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
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_nameClass I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli
experiment.sample.molecule[0].short_nameFbaB
experiment.sample.molecule[0].sequenceMTDIAQLLGKDADNLLQHCCMTIPSDQLYLPGHDYVDRVMIDNNRPPAVLRNMQTLYNTG RLAGTGYLSILPVDQGVEHSAGASFAANPLYFDPKNIVELAIEAGCNCVASTYGVLASVS RRYAHRIPFLVKLNHNETLSYPNTYDQTLYASVEQAFNMGAVAVGATIYFGSEESRRQIE EISAAFERAHELGMVTVLWAYLRNSAFKKDGVDYHVSADLTGQANHLAATIGADIVKQKM AENNGGYKAINYGYTDDRVYSKLTSENPIDLVRYQLANCYMGRAGLINSGGAAGGETDLS DAVRTAVINKRAGGMGLILGRKAFKKSMADGVKLINAVQDVYLDSKITIA
experiment.sample.molecule[0].organismEscherichia coli
experiment.sample.molecule[0].uniprot_codeA0A0K4BP99
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationdecamer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequencenull
experiment.sample.molecule[0].mw38.056
experiment.sample.molecule[0].total_mw380.557
experiment.sample.molecule[0].number_molecules10
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 10 mM NaCl
experiment.sample.buffer.concentration_unitmM
experiment.sample.buffer.commentnull
experiment.sample.buffer.additive10 mM NaCl
experiment.sample.buffer.concentration50.0
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.5
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameClass I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli
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_nameMSU
experiment.contributor[0].affiliation[0].addressMoscow, Russia
experiment.contributor[0].affiliation[0].full_nameLomonosov Moscow State University
experiment.contributor[0].affiliation[0].webpagehttp://www.msu.ru
experiment.contributor[0].contributor_nameLiubov
experiment.contributor[0].contributor_surnameDadinova
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2013-06-30
experiment.storage_temperature10.0
experiment.cell_temperature10.0
experiment.exposure_time0.05
experiment.number_of_frames20
experiment.wavelength0.12
experiment.sample_detector_distance3.1
experiment.concentration_min1.4
experiment.concentration_max10.8
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.085
experiment.s_max3.234
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].models[0].software_version
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fits[0].p_value0.00021
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fits[1].chi_square_value1.81
fits[1].p_value0.0
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fits[1].fit_lognull
fits[1].software_versionnull
fits[1].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionnull
i0_calibration_standardnull
descriptionThe models displayed above are, from top to bottom: 1) An individual DAMMIN dummy atom model and; 2) CORAL rigid body model with the associated CRYSOL fit to the data. All of the individual DAMMIN models and associated fits can be found in the zip archive for this entry along with the CORAL modelling results.
experiment_descriptionSynchrotron SAXS data from solutions of Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli in 50 mM Tris pH 7.5 were collected on the P12 beam line of Petra-III (Hamburg, Germany) using a Pilatus 2M detector (I(s) vs s; s = 4π sin θ/λ, where 2θ is the scattering angle and λ=0.124 nm). Different solute concentrations in the range 2.6-13.30 mg/ml were measured using an exposure time of 1 s (recorded as 20 x 0.050 s frames). The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering from the matched solvent-blank was subtracted. The data presented here are from a single concentration scattering curve (9.3 mg/ml).
tags[]
intensity_unitnull
experimental_mw340.0
experimental_mw_errornull
guinier_i0_mw340.0
guinier_i0_mw_errornull
porod_mw302.0
porod_mw_errornull
pddf_i016670.0
pddf_i0_error18.0
guinier_i016826.0
guinier_i0_error25.0
pddf_rg4.34
pddf_rg_error0.04
guinier_rg4.43
guinier_rg_error0.02
pddf_dmax12.73
pddf_dmax_errornull
porod_volume484.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first2
guinier_point_last81
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDBZ2_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
codeSASDBZ2
statussuccess
started_at2026-08-11T13:49:42.824397+00:00
finished_at2026-08-11T13:50:03.716442+00:00
source_last_modified2023-06-21T07:56:39.492710+02:00
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查看完整 summary.json 原文
{
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  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "X-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism.",
    "publication": {
      "title": "X-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism.",
      "author_list": "Dadinova LA, Shtykova EV, Konarev PV, Rodina EV, Snalina NE, Vorobyeva NN, Kurilova SA, Nazarova TI, Jeffries CM, Svergun DI",
      "journal": "PLoS One",
      "doi": "10.1371/journal.pone.0156105",
      "pmid": "27227414",
      "published_date": "2016"
    },
    "status": "released",
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    "released_date": "2016-07-01"
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        "resolution": null
      },
      "name": "PETRA III",
      "city": "DESY; Hamburg",
      "country": "Germany",
      "beamline_name": "EMBL P12",
      "beam_geometry": null,
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          "organism": "Escherichia coli",
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          "oligomerization": "decamer",
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      "buffer": {
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        "comment": null,
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        "concentration": 50.0,
        "pka": null,
        "ph": 7.5,
        "deuteration": null
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      "purity_method": null,
      "name": "Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli",
      "ext_coefficient": null,
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      "specific_vol": null,
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      "absorbption": null,
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    "contributor": [
      {
        "affiliation": [
          {
            "short_name": "MSU",
            "address": "Moscow, Russia",
            "full_name": "Lomonosov Moscow State University",
            "webpage": "http://www.msu.ru"
          }
        ],
        "contributor_name": "Liubov",
        "contributor_surname": "Dadinova",
        "orcid": null
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    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2013-06-30",
    "storage_temperature": 10.0,
    "cell_temperature": 10.0,
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    "number_of_frames": 20,
    "wavelength": 0.12,
    "sample_detector_distance": 3.1,
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          "software": "DAMMIN",
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          "software_version": "",
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDBZ2_fit1_model1.pdb",
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          "log": "https://www.sasbdb.org/media/log_files/2.log",
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          "user": 94
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      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBZ2_fit2_fit_img.png",
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      "fit_residual_plot": "SASDBZ2_fit2_fitresiduals_img.png",
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  "description": "The models displayed above are, from top to bottom: 1) An individual DAMMIN dummy atom model and; 2) CORAL rigid body model with the associated CRYSOL fit to the data. All of the individual DAMMIN models and associated fits can be found in the zip archive for this entry along with the CORAL modelling results.",
  "experiment_description": "Synchrotron SAXS data from solutions of Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli in 50 mM Tris pH 7.5 were collected on the P12 beam line of Petra-III (Hamburg, Germany) using a Pilatus 2M detector (I(s) vs s; s = 4π sin θ/λ, where 2θ is the scattering angle and λ=0.124 nm). Different solute concentrations in the range 2.6-13.30 mg/ml were measured using an exposure time of 1 s (recorded as 20 x 0.050 s frames). The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering from the matched solvent-blank was subtracted. The data presented here are from a single concentration scattering curve (9.3 mg/ml).",
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  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDBZ2_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2023-06-21T07:56:39.492710+02:00",
  "bragg_peak": []
}
查看完整 manifest.json 原文
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