SASDFS4

HP0242 from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain (Domain A (PDB:3MLI)-Linker (PDB:1BR0)-Domain B (PDB:4DZL))

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Extrapolated to infinite dilution 最后更新:2019-12-06T13:07:15.624532+01:00
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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · HP0242 from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain (Domain A (PDB:3MLI)-Linker (PDB:1BR0)-Domain B (PDB:4DZL))

浓度1.9 – 6.8 缓冲液 / pH20 mM Tris-HCl 150 mM NaCl / 8.0
实验温度20.0 设备 / 束线Nara Institute of Science and Technology / Rigaku Nano-Viewer
波长0.15418 nm曝光60.0 s × 25

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
HP0242 from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain
查看序列
MGSSHHHHHHSSGLVPRGSHMRDYSELEIFEGNPLDKWNDIIFHASKKASKKELERLLELLALCETFIEKEDLEEKFESFAKALRIDEELQQKIESRKTDIVIQSMANILSALFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSAILASPNPDEKTKEELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQHSTLSRKFVEVMSEYNATQSDYGSGGEIAAIKQEIAAIKKEIAAIKWEIAAIKQGYG
proteinHelicobacter pylori, Rattus norvegicus, de novo design——–—hexamer分子数 629.855 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
1312[3]0.01382–0.300346 1/A含误差列缺失 015sasbdb/entries/s4/sasdfs4/source/SASDFS4.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)24.0—Å
i0Guinier40.113.11arbitrary
i0P(r)40.92.2arbitrary
mwExperimental187.0—kDa
mwGuinier I(0)187.010.0kDa
mwPorod401.0—kDa
porod_volumePorod642.0—ų
rgGuinier6.530.6Å
rgP(r)7.00.3Å

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20 mM Tris-HCl 150 mM NaCl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2017-03-29储存 / 测量温度4.0 / 20.0
曝光时间60.0帧数25
波长0.15418样品-探测器距离0.75
光源X-ray in house探测器Pilatus 200K
机构 / 束线Nara Institute of Science and Technology / Rigaku Nano-Viewer · Ikoma, Japan
q 范围0.138 – 3.003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/s4/sasdfs4/source/SASDFS4.zipdownloaded202786d0fcb887e5a0fee35e6b2f80c04880119485d5b046497644f46530448eaa382b下载查看原文件源站
pddfsasbdb/entries/s4/sasdfs4/source/SASDFS4.outdownloaded2521798d60e71850e0a7a97c672061e130e23ff03e4a54739d4d3f2d4771114f94fc2下载查看原文件源站
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summarysasbdb/entries/s4/sasdfs4/source/summary.jsondownloaded829422c4d7ff3a17f18ba28357c235db518ee91f75ac838392746b35c2c6fef1a1d7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(4 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:167 个字段值
字段路径原始值
codeSASDFS4
statusPublished
type_of_curveExtrapolated to infinite dilution
angular_unit1/A
project.titleConstruction of a Quadrangular Tetramer and a Cage-Like Hexamer from Three-Helix Bundle-Linked Fusion Proteins.
project.publication.titleConstruction of a Quadrangular Tetramer and a Cage-Like Hexamer from Three-Helix Bundle-Linked Fusion Proteins.
project.publication.author_listMiyamoto T, Hayashi Y, Yoshida K, Watanabe H, Uchihashi T, Yonezawa K, Shimizu N, Kamikubo H, Hirota S
project.publication.journalACS Synth Biol
project.publication.doi10.1021/acssynbio.9b00019
project.publication.pmid30966743
project.publication.published_date2019 Apr 16
project.statusreleased
project.submitted_date2019-03-28
project.released_date2019-04-24
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intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDFS4.dat
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sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDFS4.sascif
experiment.instrument.detector.typePilatus
experiment.instrument.detector.namePilatus 200K
experiment.instrument.detector.resolution172.0
experiment.instrument.nameNara Institute of Science and Technology
experiment.instrument.cityIkoma
experiment.instrument.countryJapan
experiment.instrument.beamline_nameRigaku Nano-Viewer
experiment.instrument.beam_geometrynull
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_nameHP0242 from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain
experiment.sample.molecule[0].short_nameFusion protein2
experiment.sample.molecule[0].sequenceMGSSHHHHHHSSGLVPRGSHMRDYSELEIFEGNPLDKWNDIIFHASKKASKKELERLLELLALCETFIEKEDLEEKFESFAKALRIDEELQQKIESRKTDIVIQSMANILSALFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSAILASPNPDEKTKEELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQHSTLSRKFVEVMSEYNATQSDYGSGGEIAAIKQEIAAIKKEIAAIKWEIAAIKQGYG
experiment.sample.molecule[0].organismHelicobacter pylori, Rattus norvegicus, de novo design
experiment.sample.molecule[0].uniprot_codenull
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationhexamer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequencenull
experiment.sample.molecule[0].mw29.855
experiment.sample.molecule[0].total_mw179.13
experiment.sample.molecule[0].number_molecules6
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.name20 mM Tris-HCl 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.ph8.0
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameHP0242 from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain (Domain A (PDB:3MLI)-Linker (PDB:1BR0)-Domain B (PDB:4DZL))
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].addressJapan
experiment.contributor[0].affiliation[0].full_nameNara Institute of Science and Technology
experiment.contributor[0].affiliation[0].webpagehttp://www.naist.jp/en/
experiment.contributor[0].contributor_nameHironari
experiment.contributor[0].contributor_surnameKamikubo
experiment.contributor[0].orcidhttps://orcid.org/0000-0002-0878-6488
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2017-03-29
experiment.storage_temperature4.0
experiment.cell_temperature20.0
experiment.exposure_time60.0
experiment.number_of_frames25
experiment.wavelength0.15418
experiment.sample_detector_distance0.75
experiment.concentration_min1.9
experiment.concentration_max6.8
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.138
experiment.s_max3.003
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].softwareCORAL
fits[0].models[0].pdb_link[0].pdb_code3mli
fits[0].models[0].pdb_link[0].ext_code3MLI
fits[0].models[0].pdb_link[0].ext_typepdb
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fits[0].models[0].model_mw180.1
fits[0].models[0].bead_radius1.9
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fits[0].models[0].symmetrynull
fits[0].models[0].commentnull
fits[0].models[0].user432
fits[0].fit_unit1/A
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fits[0].softwareCORAL
fits[0].chi_square_value0.1
fits[0].p_value8.8e-05
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fits[0].software_version5
fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSAXS data from solutions of the fusion protein2 in 20 mM Tris-HCl, 150 mM KCl, pH 8.0 were collected using a Nano-Viewer (Rigaku, Japan) at NAIST (Nara, Japan) equipped with a Pilatus 200K detector at a sample-detector distance of 0.75 m and at a wavelength of λ = 0.15418 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Twenty-five successive 60 second frames were collected at a sample temperature of 20°C. Solute concentrations ranging between 1.9 and 6.8 mg/ml were measured. The data were normalized to the intensity of the direct beam and radially averaged. The scattering from the solvent-blank was subtracted. The scattering profile in this entry represents an extrapolation to infinite dilution.
tags[]
intensity_unitarbitrary
experimental_mw187.0
experimental_mw_errornull
guinier_i0_mw187.0
guinier_i0_mw_error10.0
porod_mw401.0
porod_mw_errornull
pddf_i040.9
pddf_i0_error2.2
guinier_i040.11
guinier_i0_error3.11
pddf_rg7.0
pddf_rg_error0.3
guinier_rg6.53
guinier_rg_error0.6
pddf_dmax24.0
pddf_dmax_errornull
porod_volume642.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first1
guinier_point_last8
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDFS4_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
codeSASDFS4
statussuccess
started_at2026-08-11T14:30:05.467496+00:00
finished_at2026-08-11T14:30:14.733204+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": "SASDFS4",
  "status": "Published",
  "type_of_curve": "Extrapolated to infinite dilution",
  "angular_unit": "1/A",
  "project": {
    "title": "Construction of a Quadrangular Tetramer and a Cage-Like Hexamer from Three-Helix Bundle-Linked Fusion Proteins.",
    "publication": {
      "title": "Construction of a Quadrangular Tetramer and a Cage-Like Hexamer from Three-Helix Bundle-Linked Fusion Proteins.",
      "author_list": "Miyamoto T, Hayashi Y, Yoshida K, Watanabe H, Uchihashi T, Yonezawa K, Shimizu N, Kamikubo H, Hirota S",
      "journal": "ACS Synth Biol",
      "doi": "10.1021/acssynbio.9b00019",
      "pmid": "30966743",
      "published_date": "2019 Apr 16"
    },
    "status": "released",
    "submitted_date": "2019-03-28",
    "released_date": "2019-04-24"
  },
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      "country": "Japan",
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          "long_name": "HP0242 from Helicobacter pylori,  N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain",
          "short_name": "Fusion protein2",
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      "name": "HP0242 from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain (Domain A (PDB:3MLI)-Linker (PDB:1BR0)-Domain B (PDB:4DZL))",
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            "short_name": null,
            "address": "Japan",
            "full_name": "Nara Institute of Science and Technology",
            "webpage": "http://www.naist.jp/en/"
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        "contributor_name": "Hironari",
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    "concentration_unit": null,
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  "last_modified": "2019-12-06T13:07:15.624532+01:00",
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}
查看完整 manifest.json 原文
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