SASDEK4

C-terminal catalytic domain of Suppressor of Copper Sensitivity C protein (ScsC)

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Single concentration 最后更新:2020-06-15T11:37:11.282615+02:00
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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · C-terminal catalytic domain of Suppressor of Copper Sensitivity C protein (ScsC)

浓度— – 0.5 缓冲液 / pH10mM HEPES, 150mM NaCl / 7.4
实验温度10.0 设备 / 束线Australian Synchrotron / SAXS/WAXS
波长0.1033 nm曝光1.0 s × 38

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
C-terminal catalytic domain of Suppressor of Copper Sensitivity C protein
查看序列
SNAQFRQALASEHDALYNDAASPRIGAKDAKLVLVSFTDYNCPYCKRFDPLLEKITEQYPDVAVIIKPLPFKGESSAKASQAVLSVWKEDPKAFLALHQRLMQKKTMLDNASIEDAMKSTNTSKIKLTDDSLKTLQNNLELSRKLGIQGTPATVIGDTILPGAVDYDQLEIIVKEQLAKVKK
proteinProteus mirabilisA0A1Z1SYD564–243monomer分子数 120.15 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
1295[3]0.0159736425–0.3633577228 1/A含误差列缺失 030sasbdb/entries/k4/sasdek4/source/SASDEK4.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)5.4—Å
i0Guinier0.0040551e-061/cm
i0P(r)0.004053—1/cm
mwExperimental19.0—kDa
mwGuinier I(0)11.02.0kDa
mwPorod19.0—kDa
porod_volumePorod22200.0—ų
rgGuinier1.70.01Å
rgP(r)1.69—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

拟合 1 · DAMMIN 5.3

χ²:1.079CorMap p:0.24638单位:1/A

Representative example of 1 of 16 dummy atom modelling optimisations.

模型名称 / 类型软件对称性模型 MWPDB 声明来源文件
1—dummyDAMFILT 5.0P116.086—模型 图片

拟合 2 · CRYSOL 2.8.3

χ²:1.12CorMap p:0.017618单位:1/A
模型名称 / 类型软件对称性模型 MWPDB 声明来源文件
1—atomicPDB (Protein Data Bank) P119.724YX8本库暂无,前往 RCSB PDB模型 图片
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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10mM HEPES, 150mM NaCl缓冲液浓度—
pH7.4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2018-04-05储存 / 测量温度4.0 / 10.0
曝光时间1.0帧数38
波长0.1033样品-探测器距离3.33
光源X-ray synchrotron探测器Pilatus 1M
机构 / 束线Australian Synchrotron / SAXS/WAXS · Melbourne, Australia
q 范围0.16 – 3.634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/k4/sasdek4/source/SASDEK4.zipdownloaded67516e2f8c07a7012ef790ac104be0ebf108b23db4f4fa3c4e5ce4b47bfe2f3e6f8b4下载查看原文件源站
pddfsasbdb/entries/k4/sasdek4/source/SASDEK4.outdownloaded25679245274799716eb7f855c07b6e2e697b15d479c660109a2e8e3c7c0dbad4e2d2e下载查看原文件源站
sascifsasbdb/entries/k4/sasdek4/source/SASDEK4.sascifdownloaded380068e68de39bbb31dca47a95e652b3ed658260e30c31e52722c66747714658c2cc53下载查看原文件源站
summarysasbdb/entries/k4/sasdek4/source/summary.jsondownloaded909574c606f854a9b5f4dcffa48d79522d45ea94c14e65acf3ed8e76b1df231169ed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(6 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:182 个字段值
字段路径原始值
codeSASDEK4
statusPublished
type_of_curveSingle concentration
angular_unit1/A
project.titleEngineered variants provide new insight into the structural properties important for activity of the highly dynamic, trimeric protein disulfide isomerase ScsC from Proteus mirabilis.
project.publication.titleEngineered variants provide new insight into the structural properties important for activity of the highly dynamic, trimeric protein disulfide isomerase ScsC from Proteus mirabilis.
project.publication.author_listFurlong EJ, Kurth F, Premkumar L, Whitten AE, Martin JL
project.publication.journalActa Crystallogr D Struct Biol
project.publication.doi10.1107/S2059798319000081
project.publication.pmid30950400
project.publication.published_date2019 Mar 1
project.statusreleased
project.submitted_date2018-09-18
project.released_date2019-03-29
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDEK4.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDEK4.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEK4_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEK4_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEK4_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEK4_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDEK4.sascif
experiment.instrument.detector.typeDectris
experiment.instrument.detector.namePilatus 1M
experiment.instrument.detector.resolution172.0
experiment.instrument.nameAustralian Synchrotron
experiment.instrument.cityMelbourne
experiment.instrument.countryAustralia
experiment.instrument.beamline_nameSAXS/WAXS
experiment.instrument.beam_geometryPoint
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourceTrue
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_nameC-terminal catalytic domain of Suppressor of Copper Sensitivity C protein
experiment.sample.molecule[0].short_namePmScsCΔN
experiment.sample.molecule[0].sequenceSNAQFRQALASEHDALYNDAASPRIGAKDAKLVLVSFTDYNCPYCKRFDPLLEKITEQYPDVAVIIKPLPFKGESSAKASQAVLSVWKEDPKAFLALHQRLMQKKTMLDNASIEDAMKSTNTSKIKLTDDSLKTLQNNLELSRKLGIQGTPATVIGDTILPGAVDYDQLEIIVKEQLAKVKK
experiment.sample.molecule[0].organismProteus mirabilis
experiment.sample.molecule[0].uniprot_codeA0A1Z1SYD5
experiment.sample.molecule[0].uniprot_range_first64
experiment.sample.molecule[0].uniprot_range_last243
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMKKTLSVLVISSLLFGANVQAAALNAAQEKEVRALVRDTLVSNPEILEEAIMALQTKKAD EQQAQFRQALASEHDALYNDAASPRIGAKDAKLVLVSFTDYNCPYCKRFDPLLEKITEQY PDVAVIIKPLPFKGESSAKASQAVLSVWKEDPKAFLALHQRLMQKKTMLDNASIEDAMKS TNTSKIKLTDDSLKTLQNNLELSRKLGIQGTPATVIGDTILPGAVDYDQLEIIVKEQLAK VKK
experiment.sample.molecule[0].mw20.15
experiment.sample.molecule[0].total_mw20.15
experiment.sample.molecule[0].number_molecules1
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.name10mM HEPES, 150mM 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.ph7.4
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameC-terminal catalytic domain of Suppressor of Copper Sensitivity C protein (ScsC)
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_nameANSTO
experiment.contributor[0].affiliation[0].addressKirrawee DC, NSW 2232, Australia
experiment.contributor[0].affiliation[0].full_nameAustralian Nuclear Science and Technology Organisation
experiment.contributor[0].affiliation[0].webpage
experiment.contributor[0].contributor_nameAndrew
experiment.contributor[0].contributor_surnameWhitten
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2018-04-05
experiment.storage_temperature4.0
experiment.cell_temperature10.0
experiment.exposure_time1.0
experiment.number_of_frames38
experiment.wavelength0.1033
experiment.sample_detector_distance3.33
experiment.concentration_minnull
experiment.concentration_max0.5
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.16
experiment.s_max3.634
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDEK4_fit1_model1_img.png
fits[0].models[0].softwareDAMFILT
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modeldummy
fits[0].models[0].software_version5.0
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fits[0].models[0].model_mw16.086
fits[0].models[0].bead_radius1.5
fits[0].models[0].lognull
fits[0].models[0].symmetryP1
fits[0].models[0].commentnull
fits[0].models[0].user111
fits[0].fit_unit1/A
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fits[0].softwareDAMMIN
fits[0].chi_square_value1.079
fits[0].p_value0.24638
fits[0].fit_residual_plotrun1_fitresiduals_img.png
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fits[0].fit_loghttps://www.sasbdb.org/media/fitting_files/log_files/run1_WKbXguT.log
fits[0].software_version5.3
fits[0].descriptionRepresentative example of 1 of 16 dummy atom modelling optimisations.
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fits[1].models[0].softwarePDB (Protein Data Bank)
fits[1].models[0].pdb_link[0].pdb_code4yx8
fits[1].models[0].pdb_link[0].ext_code4YX8
fits[1].models[0].pdb_link[0].ext_typepdb
fits[1].models[0].pdb_link[0].difference_with_modelidentical
fits[1].models[0].model_titlenull
fits[1].models[0].type_of_modelatomic
fits[1].models[0].software_versionnull
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fits[1].models[0].model_mw19.72
fits[1].models[0].bead_radiusnull
fits[1].models[0].lognull
fits[1].models[0].symmetryP1
fits[1].models[0].commentnull
fits[1].models[0].user111
fits[1].fit_unit1/A
fits[1].fit_plothttps://www.sasbdb.org/media/fitting_files/scattering_plots/PmScsCDN01_fit_img.png
fits[1].softwareCRYSOL
fits[1].chi_square_value1.12
fits[1].p_value0.017618
fits[1].fit_residual_plotnull
fits[1].fit_datahttps://www.sasbdb.org/media/fitting_files/SASDEK4_fit2.fit
fits[1].fit_loghttps://www.sasbdb.org/media/fitting_files/log_files/PmScsCDN01.log
fits[1].software_version2.8.3
fits[1].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version4.6
i0_calibration_standardnull
descriptionnull
experiment_descriptionX-ray synchrotron radiation scattering data from solutions of the C-terminal catalytic domain of Suppressor of Copper Sensitivity C protein (ScsC) protein from Proteus mirabilis in 10 mM HEPES 150mM NaCl, pH 7.4 were collected on the SAXS/WAXS beam line of the Australian Synchrotron (Melbourne, Australia) using a 2D Photon counting Pilatus 1M-W pixel detector (s = 4π sin θ/λ, where 2θ is the scattering angle). Thirty eight successive 1 second frames were collected across solute concentrations of 0.1-10.0 mg/ml at a sample temperature of 10°C. The SAXS data displayed this entry was derived from a 0.50 mg/ml sample. The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering of the solvent-blank was subtracted.
tags[]
intensity_unit1/cm
experimental_mw19.0
experimental_mw_errornull
guinier_i0_mw11.0
guinier_i0_mw_error2.0
porod_mw19.0
porod_mw_errornull
pddf_i00.004053
pddf_i0_errornull
guinier_i00.004055
guinier_i0_error1e-06
pddf_rg1.69
pddf_rg_errornull
guinier_rg1.7
guinier_rg_error0.01
pddf_dmax5.4
pddf_dmax_errornull
porod_volume22200.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first1
guinier_point_last52
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDEK4_datloglog_img.png
symmetrynull
last_modified2020-06-15T11:37:11.282615+02:00
bragg_peak[]
manifest.json:36 个字段值
字段路径原始值
codeSASDEK4
statussuccess
started_at2026-08-11T16:25:16.687044+00:00
finished_at2026-08-11T16:25:25.450757+00:00
source_last_modified2020-06-15T11:37:11.282615+02:00
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files[4].zip_validationcentral_directory_readable
查看完整 summary.json 原文
{
  "code": "SASDEK4",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/A",
  "project": {
    "title": "Engineered variants provide new insight into the structural properties important for activity of the highly dynamic, trimeric protein disulfide isomerase ScsC from Proteus mirabilis.",
    "publication": {
      "title": "Engineered variants provide new insight into the structural properties important for activity of the highly dynamic, trimeric protein disulfide isomerase ScsC from Proteus mirabilis.",
      "author_list": "Furlong EJ, Kurth F, Premkumar L, Whitten AE, Martin JL",
      "journal": "Acta Crystallogr D Struct Biol",
      "doi": "10.1107/S2059798319000081",
      "pmid": "30950400",
      "published_date": "2019 Mar 1"
    },
    "status": "released",
    "submitted_date": "2018-09-18",
    "released_date": "2019-03-29"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEK4.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEK4.dat",
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  "last_modified": "2020-06-15T11:37:11.282615+02:00",
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}
查看完整 manifest.json 原文
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