SASDDT5

Ribonucleoprotein complex of nonstructural protein sigma NS bound to 20mer RNA (NS-RNP20)

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Merged 最后更新:2019-12-06T13:07:15.624532+01:00

SigmaNS ribonucleoprotein complex with 20mer RNA. Sample concentration, UNKNOWN; Sample temperature, UNKNOWN; Exposure time; UNKNOWN.

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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Ribonucleoprotein complex of nonstructural protein sigma NS bound to 20mer RNA (NS-RNP20)

浓度— – — 缓冲液 / pH25 mM HEPES, 150 mM NaCl / 7.5
实验温度— 设备 / 束线Diamond Light Source / B21
波长0.1 nm曝光— s × —

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
Nonstructural protein sigma NS
查看序列
MDNTVRVGVSRNTSGAAGQTLFRNFYLLRCNISADGRNATKAVQSHFPFLSRAVRCLSPLAAHCADRTLRRDNVKQILTRELPFSSDLINYAHHVNSSSLTTSQGVEAARLVAQVYGEQVPFDHIYPTGSATYCPGAIANAISRIMAGFVPREGDDFAPSGPIDYLAADLIAYKFVLPYMLDMVDGRPQIVLPSHTVEEMLTNTSLLNSIDASFGIEARSDQRMTRDAAEMSSRSLNELEDHDQRGRMPWKIMLAMMAAQLKVELDALADERTESQANAHVTSFGSRLFNQMSAFVTIDRELMELALLIKEQGFAMNPGQIASKWSLIRRSGPTRPLSGARLEIRNGNWMIREGDQTLLSVSPARMA
proteinAvian orthoreovirusQ9DH28—–—octamer分子数 840.586 kDa
20mer RNA (unstructured)
查看序列
CUUUUCAAGACAUGCAACAA
RNA———–—dimer分子数 26.399 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
11662[3]0.0037–0.37 1/A含误差列缺失 0278sasbdb/entries/t5/sasddt5/source/SASDDT5.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)38.0—Å
i0Guinier0.29910.001arbitrary
i0P(r)0.3067—arbitrary
mwExperimental323.0—kDa
porod_volumePorod964.0—ų
rgGuinier7.820.06Å
rgP(r)8.65—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

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25 mM HEPES, 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2017-02-25储存 / 测量温度— / —
曝光时间—帧数—
波长0.1样品-探测器距离3.9
光源X-ray synchrotron探测器Pilatus 2M
机构 / 束线Diamond Light Source / B21 · Didcot, UK
q 范围0.037 – 3.7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/t5/sasddt5/source/SASDDT5.zipdownloaded44731524fbae3a52614d98a4d4f5538775755413dcdf64e5b36594597a65a2b599609下载查看原文件源站
pddfsasbdb/entries/t5/sasddt5/source/SASDDT5.outdownloaded9289472cd43d802c48434d1796b6999974360e2e07ea3e783932553f2b86a81c7a6e0下载查看原文件源站
sascifsasbdb/entries/t5/sasddt5/source/SASDDT5.sascifdownloaded151844766d40ef11a78381114219001ba79837171711910f957491804ffd5b4862cabf下载查看原文件源站
summarysasbdb/entries/t5/sasddt5/source/summary.jsondownloaded730988e1a731f5256adf3cbf0db468703e1b42cbe854a9fa6b78a7f0bebd22bce59e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
codeSASDDT5
statusPublished
type_of_curveMerged
angular_unit1/A
project.titleStability of local secondary structure determines selectivity of viral RNA chaperones.
project.publication.titleStability of local secondary structure determines selectivity of viral RNA chaperones.
project.publication.author_listBravo JPK, Borodavka A, Barth A, Calabrese AN, Mojzes P, Cockburn JJB, Lamb DC, Tuma R
project.publication.journalNucleic Acids Res
project.publication.doi10.1093/nar/gky394
project.publication.pmid29796667
project.publication.published_date2018 May 18
project.statusreleased
project.submitted_date2018-04-01
project.released_date2018-04-26
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDDT5.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDDT5.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDT5_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDT5_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDT5_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDT5_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDDT5.sascif
experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus 2M
experiment.instrument.detector.resolutionnull
experiment.instrument.nameDiamond Light Source
experiment.instrument.cityDidcot
experiment.instrument.countryUK
experiment.instrument.beamline_nameB21
experiment.instrument.beam_geometry1 x 5 mm
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_nameNonstructural protein sigma NS
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceMDNTVRVGVSRNTSGAAGQTLFRNFYLLRCNISADGRNATKAVQSHFPFLSRAVRCLSPL AAHCADRTLRRDNVKQILTRELPFSSDLINYAHHVNSSSLTTSQGVEAARLVAQVYGEQV PFDHIYPTGSATYCPGAIANAISRIMAGFVPREGDDFAPSGPIDYLAADLIAYKFVLPYM LDMVDGRPQIVLPSHTVEEMLTNTSLLNSIDASFGIEARSDQRMTRDAAEMSSRSLNELE DHDQRGRMPWKIMLAMMAAQLKVELDALADERTESQANAHVTSFGSRLFNQMSAFVTIDR ELMELALLIKEQGFAMNPGQIASKWSLIRRSGPTRPLSGARLEIRNGNWMIREGDQTLLS VSPARMA
experiment.sample.molecule[0].organismAvian orthoreovirus
experiment.sample.molecule[0].uniprot_codeQ9DH28
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationoctamer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMDNTVRVGVSRNTSGAAGQTLFRNFYLLRCNISADGRNATKAVQSHFPFLSRAVRCLSPL AAHCADRTLRRDNVKQILTRELPFSSDLINYAHHVNSSSLTTSQGVEAARLVAQVYGEQV PFDHIYPTGSATYCPGAIANAISRIMAGFVPREGDDFAPSGPIDYLAADLIAYKFVLPYM LDMVDGRPQIVLPSHTVEEMLTNTSLLNSIDASFGIEARSDQRMTRDAAEMSSRSLNELE DHDQRGRMPWKIMLAMMAAQLKVELDALADERTESQANAHVTSFGSRLFNQMSAFVTIDR ELMELALLIKEQGFAMNPGQIASKWSLIRRSGPTRPLSGARLEIRNGNWMIREGDQTLLS VSPARMA
experiment.sample.molecule[0].mw40.586
experiment.sample.molecule[0].total_mw324.688
experiment.sample.molecule[0].number_molecules8
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_name20mer RNA (unstructured)
experiment.sample.molecule[1].short_name20mer
experiment.sample.molecule[1].sequenceCUUUUCAAGACAUGCAACAA
experiment.sample.molecule[1].organismnull
experiment.sample.molecule[1].uniprot_codenull
experiment.sample.molecule[1].uniprot_range_firstnull
experiment.sample.molecule[1].uniprot_range_lastnull
experiment.sample.molecule[1].oligomerizationdimer
experiment.sample.molecule[1].molecular_typeRNA
experiment.sample.molecule[1].uniprot_sequencenull
experiment.sample.molecule[1].mw6.399
experiment.sample.molecule[1].total_mw12.798
experiment.sample.molecule[1].number_molecules2
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.name25 mM HEPES, 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.nameRibonucleoprotein complex of nonstructural protein sigma NS bound to 20mer RNA (NS-RNP20)
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].addressLeeds, UK
experiment.contributor[0].affiliation[0].full_nameUniversity of Leeds
experiment.contributor[0].affiliation[0].webpagehttps://www.leeds.ac.uk/
experiment.contributor[0].contributor_nameJack
experiment.contributor[0].contributor_surnameBravo
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2017-02-25
experiment.storage_temperaturenull
experiment.cell_temperaturenull
experiment.exposure_timenull
experiment.number_of_framesnull
experiment.wavelength0.1
experiment.sample_detector_distance3.9
experiment.concentration_minnull
experiment.concentration_maxnull
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.037
experiment.s_max3.7
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[]
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionSigmaNS ribonucleoprotein complex with 20mer RNA. Sample concentration, UNKNOWN; Sample temperature, UNKNOWN; Exposure time; UNKNOWN.
experiment_descriptionSynchrotron SAXS data from solutions of ribonucleoprotein complex of nonstructural protein sigma NS bound to 20mer RNA (NS-RNP20) in 25 mM HEPES, 150 mM NaCl, pH 7.5 were collected on the B21 beam line at the Diamond Light Source storage ring (Oxfordshire, UK) using a Pilatus 2M detector at a sample-detector distance of 3.9 m and at a wavelength of λ = 0.1 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). 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_mw323.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i00.3067
pddf_i0_errornull
guinier_i00.2991
guinier_i0_error0.001
pddf_rg8.65
pddf_rg_errornull
guinier_rg7.82
guinier_rg_error0.06
pddf_dmax38.0
pddf_dmax_errornull
porod_volume964.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first11
guinier_point_last45
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDDT5_datloglog_img.png
symmetrynull
last_modified2019-12-06T13:07:15.624532+01:00
bragg_peak[]
manifest.json:36 个字段值
字段路径原始值
codeSASDDT5
statussuccess
started_at2026-08-11T14:55:34.932583+00:00
finished_at2026-08-11T14:55:44.307433+00:00
source_last_modified2019-12-06T13:07:15.624532+01:00
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查看完整 summary.json 原文
{
  "code": "SASDDT5",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/A",
  "project": {
    "title": "Stability of local secondary structure determines selectivity of viral RNA chaperones.",
    "publication": {
      "title": "Stability of local secondary structure determines selectivity of viral RNA chaperones.",
      "author_list": "Bravo JPK, Borodavka A, Barth A, Calabrese AN, Mojzes P, Cockburn JJB, Lamb DC, Tuma R",
      "journal": "Nucleic Acids Res",
      "doi": "10.1093/nar/gky394",
      "pmid": "29796667",
      "published_date": "2018 May 18"
    },
    "status": "released",
    "submitted_date": "2018-04-01",
    "released_date": "2018-04-26"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDT5.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDT5.dat",
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        "name": "Pilatus 2M",
        "resolution": null
      },
      "name": "Diamond Light Source",
      "city": "Didcot",
      "country": "UK",
      "beamline_name": "B21",
      "beam_geometry": "1 x 5 mm",
      "type_of_source": "X-ray synchrotron",
      "point_source": null,
      "line_collimation": null,
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      "xray_energy": null,
      "beam_profile_ah": null,
      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
        {
          "long_name": "Nonstructural protein sigma NS",
          "short_name": null,
          "sequence": "MDNTVRVGVSRNTSGAAGQTLFRNFYLLRCNISADGRNATKAVQSHFPFLSRAVRCLSPL\r\nAAHCADRTLRRDNVKQILTRELPFSSDLINYAHHVNSSSLTTSQGVEAARLVAQVYGEQV\r\nPFDHIYPTGSATYCPGAIANAISRIMAGFVPREGDDFAPSGPIDYLAADLIAYKFVLPYM\r\nLDMVDGRPQIVLPSHTVEEMLTNTSLLNSIDASFGIEARSDQRMTRDAAEMSSRSLNELE\r\nDHDQRGRMPWKIMLAMMAAQLKVELDALADERTESQANAHVTSFGSRLFNQMSAFVTIDR\r\nELMELALLIKEQGFAMNPGQIASKWSLIRRSGPTRPLSGARLEIRNGNWMIREGDQTLLS\r\nVSPARMA",
          "organism": "Avian orthoreovirus",
          "uniprot_code": "Q9DH28",
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "octamer",
          "molecular_type": "protein",
          "uniprot_sequence": "MDNTVRVGVSRNTSGAAGQTLFRNFYLLRCNISADGRNATKAVQSHFPFLSRAVRCLSPL\nAAHCADRTLRRDNVKQILTRELPFSSDLINYAHHVNSSSLTTSQGVEAARLVAQVYGEQV\nPFDHIYPTGSATYCPGAIANAISRIMAGFVPREGDDFAPSGPIDYLAADLIAYKFVLPYM\nLDMVDGRPQIVLPSHTVEEMLTNTSLLNSIDASFGIEARSDQRMTRDAAEMSSRSLNELE\nDHDQRGRMPWKIMLAMMAAQLKVELDALADERTESQANAHVTSFGSRLFNQMSAFVTIDR\nELMELALLIKEQGFAMNPGQIASKWSLIRRSGPTRPLSGARLEIRNGNWMIREGDQTLLS\nVSPARMA",
          "mw": 40.586,
          "total_mw": 324.688,
          "number_molecules": 8,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        },
        {
          "long_name": "20mer RNA (unstructured)",
          "short_name": "20mer",
          "sequence": "CUUUUCAAGACAUGCAACAA",
          "organism": null,
          "uniprot_code": null,
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "dimer",
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          "uniprot_sequence": null,
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          "deuteration": null,
          "molecule_source": "biological",
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      ],
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        "name": "25 mM HEPES, 150 mM NaCl",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Ribonucleoprotein complex of nonstructural protein sigma NS bound to 20mer RNA (NS-RNP20)",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Leeds, UK",
            "full_name": "University of Leeds",
            "webpage": "https://www.leeds.ac.uk/"
          }
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        "contributor_name": "Jack",
        "contributor_surname": "Bravo",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2017-02-25",
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    "exposure_time": null,
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    "seccolumn": null
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  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": "5.0",
  "i0_calibration_standard": null,
  "description": "SigmaNS ribonucleoprotein complex with 20mer RNA. Sample concentration, UNKNOWN; Sample temperature, UNKNOWN; Exposure time; UNKNOWN.",
  "experiment_description": "Synchrotron SAXS data from solutions of ribonucleoprotein complex of nonstructural protein sigma NS bound to 20mer RNA (NS-RNP20) in 25 mM HEPES, 150 mM NaCl, pH 7.5 were collected on the B21 beam line at the Diamond Light Source storage ring (Oxfordshire, UK) using a Pilatus 2M detector at a sample-detector distance of 3.9 m and at a wavelength of λ = 0.1 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.",
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  "guinier_point_first": 11,
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  "pddf_point_first": null,
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  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDDT5_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
  "bragg_peak": []
}
查看完整 manifest.json 原文
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