SASDC98

Surface presentation of antigens protein SpaOc-SpaO N-terminus

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
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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Surface presentation of antigens protein SpaOc-SpaO N-terminus

浓度— – 9.5 缓冲液 / pH20 mM HEPES pH 7.5, 150 mM NaCl / 7.5
实验温度20.0 设备 / 束线PETRA III / EMBL P12
波长0.124 nm曝光— s × 3600

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
Surface presentation of antigens protein SpaO SpaO(SPOA2)
查看序列
METLDIQHIEEENNTTETAETLPGLNQLPVKLEFVLYRKNVTLAELEAMGQQQLLSLPTNAELNVEIMANGVLLGNGELVQMNDTLGVEIHEWLSESGNGESAWSHPQFEK
proteinSalmonella enterica subsp. enterica serovar TyphimuriumP40699203–303dimer分子数 212.374 kDa
Surface presentation of antigens protein SpaO(SPOA1,2) N-terminus
查看序列
MSLRVRQIDRREWLLAQTATECQRHGREATLEYPTRQGMWVRLSDAEKRWSAWIKPGDWLEHVSPALAGAAVSAGAEHLVVPWLAATERPFELPVPHLSCRRLCVENPVPGSALPEGKLLHIMSDRGGLWFEHLPELPAVGGGRPSAWSHPQFEK
proteinSalmonella enterica subsp. enterica serovar TyphimuriumP406991–145monomer分子数 117.423 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
11763[3]0.185236–5.02537 1/nm含误差列缺失 014sasbdb/entries/98/sasdc98/source/SASDC98.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)10.64—nm
i0Guinier4759.411.0arbitrary
i0P(r)4847.07.5arbitrary
mwExperimental36.3—kDa
porod_volumePorod68.0—nm³
rgGuinier2.930.008nm
rgP(r)3.060.005nm

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

该条目没有来源拟合记录。

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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20 mM HEPES pH 7.5, 150 mM NaCl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2017-04-24储存 / 测量温度20.0 / 20.0
曝光时间—帧数3600
波长0.124样品-探测器距离—
光源X-ray synchrotron探测器Pilatus 2M
机构 / 束线PETRA III / EMBL P12 · DESY; Hamburg, Germany
q 范围0.185 – 5.025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/98/sasdc98/source/SASDC98.zipdownloaded455072883a88718d55a3ea5f7ac74487178a193cda5352d81987001fe35ad09bf72ec下载查看原文件源站
pddfsasbdb/entries/98/sasdc98/source/SASDC98.outdownloaded826973aea403d85740ea87fcd869e47dbb8d8ce94b9953781ea25008c927eda17592c下载查看原文件源站
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summarysasbdb/entries/98/sasdc98/source/summary.jsondownloaded70271c3b908797d1ee18b18c4a9917434ae3861b0a1033deedbe2fe95f95590bb790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(2 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:151 个字段值
字段路径原始值
codeSASDC98
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleMolecular Organization of Soluble Type III Secretion System Sorting Platform Complexes.
project.publication.titleMolecular Organization of Soluble Type III Secretion System Sorting Platform Complexes.
project.publication.author_listBernal I, Börnicke J, Heidemann J, Svergun D, Horstmann JA, Erhardt M, Tuukkanen A, Uetrecht C, Kolbe M
project.publication.journalJ Mol Biol
project.publication.doi10.1016/j.jmb.2019.07.004
project.publication.pmid31288030
project.publication.published_date2019 Sep 6
project.statusreleased
project.submitted_date2018-11-02
project.released_date2019-09-13
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDC98.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDC98.dat
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sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDC98.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_nameSurface presentation of antigens protein SpaO SpaO(SPOA2)
experiment.sample.molecule[0].short_nameSpaOc
experiment.sample.molecule[0].sequenceMETLDIQHIEEENNTTET AETLPGLNQLPVKLEFVLYRKNVTLAELEA MGQQQLLSLPTNAELNVEIMANGVLLGNGELVQMNDTLGVEIHEWLSESGNGESAWSHPQFEK
experiment.sample.molecule[0].organismSalmonella enterica subsp. enterica serovar Typhimurium
experiment.sample.molecule[0].uniprot_codeP40699
experiment.sample.molecule[0].uniprot_range_first203
experiment.sample.molecule[0].uniprot_range_last303
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMSLRVRQIDRREWLLAQTATECQRHGREATLEYPTRQGMWVRLSDAEKRWSAWIKPGDWL EHVSPALAGAAVSAGAEHLVVPWLAATERPFELPVPHLSCRRLCVENPVPGSALPEGKLL HIMSDRGGLWFEHLPELPAVGGGRPKMLRWPLRFVIGSSDTQRSLLGRIGIGDVLLIRTS RAEVYCYAKKLGHFNRVEGGIIVETLDIQHIEEENNTTETAETLPGLNQLPVKLEFVLYR KNVTLAELEAMGQQQLLSLPTNAELNVEIMANGVLLGNGELVQMNDTLGVEIHEWLSESG NGE
experiment.sample.molecule[0].mw12.374
experiment.sample.molecule[0].total_mw24.748
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.molecule[1].long_nameSurface presentation of antigens protein SpaO(SPOA1,2) N-terminus
experiment.sample.molecule[1].short_nameSpaO N-terminus
experiment.sample.molecule[1].sequenceMSLRVRQIDRREWLLAQTATECQRHGREATLEYPTRQGMWVRLSDAEKRWSAWIKPGDWLEHVSPALAGAAVSAGAEHLVVPWLAATERPFELPVPHLSCRRLCVENPVPGSALPEGKLLHIMSDRGGLWFEHLPELPAVGGGRPSAWSHPQFEK
experiment.sample.molecule[1].organismSalmonella enterica subsp. enterica serovar Typhimurium
experiment.sample.molecule[1].uniprot_codeP40699
experiment.sample.molecule[1].uniprot_range_first1
experiment.sample.molecule[1].uniprot_range_last145
experiment.sample.molecule[1].oligomerizationmonomer
experiment.sample.molecule[1].molecular_typeprotein
experiment.sample.molecule[1].uniprot_sequenceMSLRVRQIDRREWLLAQTATECQRHGREATLEYPTRQGMWVRLSDAEKRWSAWIKPGDWL EHVSPALAGAAVSAGAEHLVVPWLAATERPFELPVPHLSCRRLCVENPVPGSALPEGKLL HIMSDRGGLWFEHLPELPAVGGGRPKMLRWPLRFVIGSSDTQRSLLGRIGIGDVLLIRTS RAEVYCYAKKLGHFNRVEGGIIVETLDIQHIEEENNTTETAETLPGLNQLPVKLEFVLYR KNVTLAELEAMGQQQLLSLPTNAELNVEIMANGVLLGNGELVQMNDTLGVEIHEWLSESG NGE
experiment.sample.molecule[1].mw17.423
experiment.sample.molecule[1].total_mw17.423
experiment.sample.molecule[1].number_molecules1
experiment.sample.molecule[1].complex_stateFalse
experiment.sample.molecule[1].deuterationnull
experiment.sample.molecule[1].molecule_sourcebiological
experiment.sample.molecule[1].molecule_descriptionnull
experiment.sample.buffer.name20 mM HEPES pH 7.5, 150 mM NaCl
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.nameSurface presentation of antigens protein SpaOc-SpaO N-terminus
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_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_nameAnne
experiment.contributor[0].contributor_surnameTuukkanen
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2017-04-24
experiment.storage_temperature20.0
experiment.cell_temperature20.0
experiment.exposure_timenull
experiment.number_of_frames3600
experiment.wavelength0.124
experiment.sample_detector_distancenull
experiment.concentration_minnull
experiment.concentration_max9.5
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.185
experiment.s_max5.025
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[]
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionnull
i0_calibration_standardnull
descriptionnull
experiment_descriptionnull
tags[]
intensity_unitarbitrary
experimental_mw36.3
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i04847.0
pddf_i0_error7.5
guinier_i04759.4
guinier_i0_error11.0
pddf_rg3.06
pddf_rg_error0.005
guinier_rg2.93
guinier_rg_error0.008
pddf_dmax10.64
pddf_dmax_errornull
porod_volume68.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first27
guinier_point_last94
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDC98_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
codeSASDC98
statussuccess
started_at2026-08-11T15:48:12.893415+00:00
finished_at2026-08-11T15:48:23.235193+00:00
source_last_modified2023-06-21T07:56:39.492710+02:00
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files[4].zip_validationcentral_directory_readable
查看完整 summary.json 原文
{
  "code": "SASDC98",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Molecular Organization of Soluble Type III Secretion System Sorting Platform Complexes.",
    "publication": {
      "title": "Molecular Organization of Soluble Type III Secretion System Sorting Platform Complexes.",
      "author_list": "Bernal I, Börnicke J, Heidemann J, Svergun D, Horstmann JA, Erhardt M, Tuukkanen A, Uetrecht C, Kolbe M",
      "journal": "J Mol Biol",
      "doi": "10.1016/j.jmb.2019.07.004",
      "pmid": "31288030",
      "published_date": "2019 Sep 6"
    },
    "status": "released",
    "submitted_date": "2018-11-02",
    "released_date": "2019-09-13"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDC98.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDC98.dat",
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  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDC98.sascif",
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        "name": "Pilatus 2M",
        "resolution": null
      },
      "name": "PETRA III",
      "city": "DESY; Hamburg",
      "country": "Germany",
      "beamline_name": "EMBL P12",
      "beam_geometry": null,
      "type_of_source": "X-ray synchrotron",
      "point_source": null,
      "line_collimation": null,
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      "xray_energy": null,
      "beam_profile_ah": null,
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    },
    "sample": {
      "molecule": [
        {
          "long_name": "Surface presentation of antigens protein SpaO SpaO(SPOA2)",
          "short_name": "SpaOc",
          "sequence": "METLDIQHIEEENNTTET AETLPGLNQLPVKLEFVLYRKNVTLAELEA \r\nMGQQQLLSLPTNAELNVEIMANGVLLGNGELVQMNDTLGVEIHEWLSESGNGESAWSHPQFEK",
          "organism": "Salmonella enterica subsp. enterica serovar Typhimurium",
          "uniprot_code": "P40699",
          "uniprot_range_first": 203,
          "uniprot_range_last": 303,
          "oligomerization": "dimer",
          "molecular_type": "protein",
          "uniprot_sequence": "MSLRVRQIDRREWLLAQTATECQRHGREATLEYPTRQGMWVRLSDAEKRWSAWIKPGDWL\nEHVSPALAGAAVSAGAEHLVVPWLAATERPFELPVPHLSCRRLCVENPVPGSALPEGKLL\nHIMSDRGGLWFEHLPELPAVGGGRPKMLRWPLRFVIGSSDTQRSLLGRIGIGDVLLIRTS\nRAEVYCYAKKLGHFNRVEGGIIVETLDIQHIEEENNTTETAETLPGLNQLPVKLEFVLYR\nKNVTLAELEAMGQQQLLSLPTNAELNVEIMANGVLLGNGELVQMNDTLGVEIHEWLSESG\nNGE",
          "mw": 12.374,
          "total_mw": 24.748,
          "number_molecules": 2,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        },
        {
          "long_name": "Surface presentation of antigens protein SpaO(SPOA1,2) N-terminus",
          "short_name": "SpaO N-terminus",
          "sequence": "MSLRVRQIDRREWLLAQTATECQRHGREATLEYPTRQGMWVRLSDAEKRWSAWIKPGDWLEHVSPALAGAAVSAGAEHLVVPWLAATERPFELPVPHLSCRRLCVENPVPGSALPEGKLLHIMSDRGGLWFEHLPELPAVGGGRPSAWSHPQFEK",
          "organism": "Salmonella enterica subsp. enterica serovar Typhimurium",
          "uniprot_code": "P40699",
          "uniprot_range_first": 1,
          "uniprot_range_last": 145,
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}
查看完整 manifest.json 原文
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