SASDB45

Trimeric periplasmic holdase chaperone protein Skp

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

The models presented above are representatives from the trimeric ensemble state(s) of Skp as determined using Ensemble Optimization Method (EOM). The Rg and size distributions obtained from EOM modelling are included in the full entry zip archive.

1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Trimeric periplasmic holdase chaperone protein Skp

浓度0.58 – 5.82 mg/ml缓冲液 / pH25 mM HEPES 150 mM NaCl 1 mM DTT / 7.5
Experimental temperature10.0 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 / OrganismUniProt 与Construct寡聚状态Molecular weight
Periplasmic holdase chaperone protein Skp
查看序列
ADKIAIVNMGSLFQQVAQKTGVSNTLENEFKGRASELQRMETDLQAKMKKLQSMKAGSDRTKLEKDVMAQRQTFAQKAQAFEQDRARRSNEERGKLVTRIQTAVKSVANSQDIDLVVDANAVAYNSSDVKDITADVLKQVK
proteinEscherichia coliP0AEU721–161trimer分子数 315.692 kDa

实验曲线

曲线点数 / 列q range误差质量负强度点来源文件
11650[3]0.096949–4.43724 1/nm含误差列缺失 00sasbdb/entries/45/sasdb45/source/SASDB45.dat

2. SASBDB 报告的指标 Reported Results

指标方法数值误差单位
dmaxP(r)12.8nm
i0Guinier4451.754.4
i0P(r)4369.029.7
mwExperimental35.0kDa
mwPorod100.0kDa
porod_volumePorod168.0nm³
rgGuinier3.570.07nm
rgP(r)3.570.02nm

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。

3. 来源拟合与模型 Source Fits & Models

4. 来源文件索引 Source Files

5. 实验说明与论文 Experiment & Publication

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“—”;Not declared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 HEPES 150 mM NaCl 1 mM DTT缓冲液浓度25.0 mM
pH7.5添加剂150 mM NaCl, 1 mM DTT
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2013-09-24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 range0.097 – 4.437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Download文件

类别文件状态大小校验值Download与查看
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full_entry_zipsasbdb/entries/45/sasdb45/source/SASDB45.zipdownloaded272800e438d078e93a709da022ea9aa1363985f34b009883d794ec7104584dc8cb43ffDownload查看原文件源站
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summarysasbdb/entries/45/sasdb45/source/summary.jsondownloaded898223b03db069eda9663560c9176e21641e71ae40750372aaac9e6350606ca5de6dDownload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(10 项)
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pddf: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
codeSASDB45
statusPublished
type_of_curveMerged
angular_unit1/nm
project.titleA Spring-Loaded Mechanism Governs the Clamp-like Dynamics of the Skp Chaperone.
project.publication.titleA Spring-Loaded Mechanism Governs the Clamp-like Dynamics of the Skp Chaperone.
project.publication.author_listHoldbrook DA, Burmann BM, Huber RG, Petoukhov MV, Svergun DI, Hiller S, Bond PJ
project.publication.journalStructure
project.publication.doi10.1016/j.str.2017.05.018
project.publication.pmid28648612
project.publication.published_date2017 Jul 5
project.statusreleased
project.submitted_date2016-07-24
project.released_date2017-06-27
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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
experiment.instrument.point_sourcenull
experiment.instrument.line_collimationnull
experiment.instrument.sample_path_lengthnull
experiment.instrument.line_collimation_slitlengthnull
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experiment.instrument.xray_energynull
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experiment.instrument.beam_profile_alnull
experiment.sample.molecule[0].long_namePeriplasmic holdase chaperone protein Skp
experiment.sample.molecule[0].short_nameSkp
experiment.sample.molecule[0].sequenceADKIAIVNMGSLFQQVAQKTGVSNTLENEFKGRASELQRMETDLQAKMKKLQSMKAGSDRTKLEKDVMAQRQTFAQKAQAFEQDRARRSNEERGKLVTRIQTAVKSVANSQDIDLVVDANAVAYNSSDVKDITADVLKQVK
experiment.sample.molecule[0].organismEscherichia coli
experiment.sample.molecule[0].uniprot_codeP0AEU7
experiment.sample.molecule[0].uniprot_range_first21
experiment.sample.molecule[0].uniprot_range_last161
experiment.sample.molecule[0].oligomerizationtrimer
experiment.sample.molecule[0].molecular_typeprotein
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experiment.sample.molecule[0].complex_stateFalse
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experiment.sample.molecule[0].molecule_sourcebiological
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experiment.sample.nameTrimeric periplasmic holdase chaperone protein Skp
experiment.sample.ext_coefficientnull
experiment.sample.contrastnull
experiment.sample.specific_volnull
experiment.sample.dry_volnull
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experiment.sample.mixturenull
experiment.contributor[0].affiliation[0].short_nameEMBL-Hamburg
experiment.contributor[0].affiliation[0].addressNotkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany
experiment.contributor[0].affiliation[0].full_nameEuropean Molecular Biology Laboratory (EMBL) - Hamburg outstation
experiment.contributor[0].affiliation[0].webpagehttp://www.embl-hamburg.de/index.php
experiment.contributor[0].contributor_nameMaxim
experiment.contributor[0].contributor_surnamePetoukhov
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitmg/ml
experiment.date2013-09-24
experiment.storage_temperature10.0
experiment.cell_temperature10.0
experiment.exposure_time0.05
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experiment.total_exposure_timenull
experiment.seccolumnnull
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i0_calibration_standardnull
descriptionThe models presented above are representatives from the trimeric ensemble state(s) of Skp as determined using Ensemble Optimization Method (EOM). The Rg and size distributions obtained from EOM modelling are included in the full entry zip archive.
experiment_descriptionX-ray synchrotron radiation scattering data from solutions of periplasmic holdase chaperone protein Skp in 25 mM HEPES 150 mM NaCl, 1 mM DTT, pH 7.5 were measured at the EMBL-P12 bioSAXS beam line on the PETRAIII storage ring (Hamburg, Germany) using a Pilatus 2M detector ((I(s) vs s, where s = 4π sin θ/λ; 2θ is the scattering angle; λ = 0.12 nm). Different solute concentrations in the range 0.58-5.82 mg/ml were measured where each sample and corresponding matched solvent blank were collected as 20 successive 50 ms frames for a total exposure time of 1 s. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the different curves were scaled for protein concentration. The low angle data collected from the 0.58 mg/ml sample were merged with the highest concentration (5.82 mg/ml) high angle data to yield the final composite scattering curve. The original SAXS data used to obtain the merged profile as displayed in this entry are included in the full entry zip archive.
tags[]
intensity_unitnull
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experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
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porod_mw_errornull
pddf_i04369.0
pddf_i0_error29.7
guinier_i04451.7
guinier_i0_error54.4
pddf_rg3.57
pddf_rg_error0.02
guinier_rg3.57
guinier_rg_error0.07
pddf_dmax12.8
pddf_dmax_errornull
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porod_volume_errornull
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estimated_volume_errornull
guinier_point_first1
guinier_point_last99
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDB45_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
codeSASDB45
statussuccess
started_at2026-08-11T14:37:35.730096+00:00
finished_at2026-08-11T14:37:45.675327+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": "SASDB45",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/nm",
  "project": {
    "title": "A Spring-Loaded Mechanism Governs the Clamp-like Dynamics of the Skp Chaperone.",
    "publication": {
      "title": "A Spring-Loaded Mechanism Governs the Clamp-like Dynamics of the Skp Chaperone.",
      "author_list": "Holdbrook DA, Burmann BM, Huber RG, Petoukhov MV, Svergun DI, Hiller S, Bond PJ",
      "journal": "Structure",
      "doi": "10.1016/j.str.2017.05.018",
      "pmid": "28648612",
      "published_date": "2017 Jul 5"
    },
    "status": "released",
    "submitted_date": "2016-07-24",
    "released_date": "2017-06-27"
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      "name": "Trimeric periplasmic holdase chaperone protein Skp",
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        "affiliation": [
          {
            "short_name": "EMBL-Hamburg",
            "address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
            "full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
            "webpage": "http://www.embl-hamburg.de/index.php"
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        "contributor_name": "Maxim",
        "contributor_surname": "Petoukhov",
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    "date": "2013-09-24",
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  "experiment_description": "X-ray synchrotron radiation scattering data from solutions of periplasmic holdase chaperone protein Skp in 25 mM HEPES 150 mM NaCl, 1 mM DTT, pH 7.5 were measured at the EMBL-P12 bioSAXS beam line on the PETRAIII storage ring (Hamburg, Germany) using a Pilatus 2M detector ((I(s) vs s, where s = 4π sin θ/λ; 2θ is the scattering angle; λ = 0.12 nm). Different solute concentrations in the range 0.58-5.82 mg/ml were measured where each sample and corresponding matched solvent blank were collected as 20 successive 50 ms frames for a total exposure time of 1 s. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the different curves were scaled for protein concentration. The low angle data collected from the 0.58 mg/ml sample were merged with the highest concentration (5.82 mg/ml) high angle data to yield the final composite scattering curve. The original SAXS data used to obtain the merged profile as displayed in this entry are included in the full entry zip archive.",
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  "last_modified": "2023-06-21T07:56:39.492710+02:00",
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}
查看完整 manifest.json 原文
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