SASDCJ7

C-terminal domain of DsbD from N. meningitidis

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Single concentration 最后更新:2021-04-10T09:51:59.686965+02:00
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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · C-terminal domain of DsbD from N. meningitidis

浓度0.3 – 4.5 缓冲液 / pH25mM HEPES 150mM NaCl / 6.7
实验温度12.0 设备 / 束线Australian Synchrotron / SAXS/WAXS
波长0.1127 nm曝光2.0 s × 30

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
DsbA-like disulfide oxidoreductase (thiol-disulfide exchange protein)
查看序列
SNAARDNVTKSKISQYKDQIFDLTYPYSGNENSSVIAVGFLDYSCGHCKAIKNDIKQLINDGKIKYIFRDAPILGNASLKAAKSALAVYFLNKEKYFDFHHAALSHKGEFSDESILDIVKNIGIDEDDFNDSIKDNADKIEQMINNSRLLVRDLGVGGTPFLIIGDSLFVGATDLNVLRKKVDELSHKQG
proteinWolbachia endosymbiont of Drosophila melanogasterQ73FL665–252monomer分子数 121.091 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
1299[3]0.0136047–0.398953 1/A含误差列缺失 00sasbdb/entries/j7/sasdcj7/source/SASDCJ7.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)4.50.3Å
i0Guinier0.009972e-051/cm
i0P(r)0.0099051.1e-051/cm
mwExperimental11.8—kDa
mwGuinier I(0)11.81.0kDa
mwPorod12.0—kDa
porod_volumePorod14.6—ų
rgGuinier1.530.01Å
rgP(r)14.80.1Å

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25mM HEPES 150mM NaCl缓冲液浓度—
pH6.7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2013-05-04储存 / 测量温度4.0 / 12.0
曝光时间2.0帧数30
波长0.1127样品-探测器距离1.48
光源X-ray synchrotron探测器Pilatus 1M
机构 / 束线Australian Synchrotron / SAXS/WAXS · Melbourne, Australia
q 范围0.136 – 3.99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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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:156 个字段值
字段路径原始值
codeSASDCJ7
statusPublished
type_of_curveSingle concentration
angular_unit1/A
project.titleProduction, biophysical characterization and initial crystallization studies of the N- and C-terminal domains of DsbD, an essential enzyme in Neisseria meningitidis.
project.publication.titleProduction, biophysical characterization and initial crystallization studies of the N- and C-terminal domains of DsbD, an essential enzyme in Neisseria meningitidis.
project.publication.author_listSmith RP, Whitten AE, Paxman JJ, Kahler CM, Scanlon MJ, Heras B
project.publication.journalActa Crystallogr F Struct Biol Commun
project.publication.doi10.1107/S2053230X17017800
project.publication.pmid29372905
project.publication.published_date2018 Jan 1
project.statusreleased
project.submitted_date2017-09-13
project.released_date2018-01-03
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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
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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_nameDsbA-like disulfide oxidoreductase (thiol-disulfide exchange protein)
experiment.sample.molecule[0].short_nameα-DsbA2
experiment.sample.molecule[0].sequenceSNAARDNVTKSKISQYKDQIFDLTYPYSGNENSSVIAVGFLDYSCGHCKAIKNDIKQLINDGKIKYIFRDAPILGNASLKAAKSALAVYFLNKEKYFDFHHAALSHKGEFSDESILDIVKNIGIDEDDFNDSIKDNADKIEQMINNSR LLVRDLGVGGTPFLIIGDSLFVGATDLNVLRKKVDELSHKQG
experiment.sample.molecule[0].organismWolbachia endosymbiont of Drosophila melanogaster
experiment.sample.molecule[0].uniprot_codeQ73FL6
experiment.sample.molecule[0].uniprot_range_first65
experiment.sample.molecule[0].uniprot_range_last252
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
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experiment.sample.molecule[0].mw21.091
experiment.sample.molecule[0].total_mw21.093
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.name25mM 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.ph6.7
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameC-terminal domain of DsbD from N. meningitidis
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.date2013-05-04
experiment.storage_temperature4.0
experiment.cell_temperature12.0
experiment.exposure_time2.0
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experiment.sample_detector_distance1.48
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experiment.flow_ratenull
experiment.s_min0.136
experiment.s_max3.99
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].softwareDAMMIN
fits[0].models[0].pdb_link[]
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fits[0].models[0].user111
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fits[0].softwareDAMMIN
fits[0].chi_square_value1.593
fits[0].p_value0.0348
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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 domain of DsbD from Neisseria meningitidis in 25 mM HEPES 150mM NaCl pH 6.7 were collected on the SAXS/WAXS beam line of the Australian Synchrotron (Melbourne, Australia) using a 2D Photon counting Pilatus 1M-W pixel detector (I(s) vs s, where s = 4π sin θ/λ and 2θ is the scattering angle; λ=0.1127 nm). Thirty successive 2 second frames were collected across solute concentrations of 0.3-4.5 mg/ml. The SAXS data displayed this entry was derived from a 1.12 mg/ml sample. The change in Rg for c-NmDsbD showed no obvious systematic trend in the concentration range measured. The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering of the solvent-blank was subtracted. The models and corresponding fits include those derived from dummy-atom modelling using DAMMIN.
tags[]
intensity_unit1/cm
experimental_mw11.8
experimental_mw_errornull
guinier_i0_mw11.8
guinier_i0_mw_error1.0
porod_mw12.0
porod_mw_errornull
pddf_i00.009905
pddf_i0_error1.1e-05
guinier_i00.00997
guinier_i0_error2e-05
pddf_rg14.8
pddf_rg_error0.1
guinier_rg1.53
guinier_rg_error0.01
pddf_dmax4.5
pddf_dmax_error0.3
porod_volume14.6
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first2
guinier_point_last44
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDCJ7_datloglog_img.png
symmetrynull
last_modified2021-04-10T09:51:59.686965+02:00
bragg_peak[]
manifest.json:36 个字段值
字段路径原始值
codeSASDCJ7
statussuccess
started_at2026-08-11T15:30:52.782754+00:00
finished_at2026-08-11T15:31:03.178383+00:00
source_last_modified2021-04-10T09:51:59.686965+02:00
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查看完整 summary.json 原文
{
  "code": "SASDCJ7",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/A",
  "project": {
    "title": "Production, biophysical characterization and initial crystallization studies of the N- and C-terminal domains of DsbD, an essential enzyme in Neisseria meningitidis.",
    "publication": {
      "title": "Production, biophysical characterization and initial crystallization studies of the N- and C-terminal domains of DsbD, an essential enzyme in Neisseria meningitidis.",
      "author_list": "Smith RP, Whitten AE, Paxman JJ, Kahler CM, Scanlon MJ, Heras B",
      "journal": "Acta Crystallogr F Struct Biol Commun",
      "doi": "10.1107/S2053230X17017800",
      "pmid": "29372905",
      "published_date": "2018 Jan 1"
    },
    "status": "released",
    "submitted_date": "2017-09-13",
    "released_date": "2018-01-03"
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            "address": "Kirrawee DC, NSW 2232, Australia",
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查看完整 manifest.json 原文
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