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SASDAB6

Xylose Isomerase

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

The data displayed at the top of the entry, and the subsequent ab inito and atomic model fit, are data derived from averaging 20 individual frames. The individual 20 data frames used for the averaging are also displayed, with the respective atomic-model fits (CRYSOL; PDB 4E3V).

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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Xylose Isomerase

浓度— – 5.76 缓冲液 / pH20 mM HEPES 200 mM Na2SO4 50 mM K2SO4 500 % v/v D2O 1 mM MgCl2 / 6.6
实验温度10.0 设备 / 束线PETRA III / EMBL P12
波长0.12 nm曝光— s × 20

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
Xylose Isomerase
查看序列
>4E3V|PDBID|COMPLETE|SEQUENCEMNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARGMNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARGMNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARGMNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG
proteinStreptomyces rubiginosus——–—tetramer分子数 443.2 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
11297[3]0.0906896–3.5006 1/nm含误差列缺失 075sasbdb/entries/b6/sasdab6/source/SASDAB6.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)9.1—nm
i0Guinier3733.8——
i0P(r)3770.0——
mwExperimental149.0—kDa
mwGuinier I(0)149.0—kDa
mwPorod137.3—kDa
porod_volumePorod233.5—nm³
rgGuinier3.21—nm
rgP(r)3.24—nm

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 HEPES 200 mM Na2SO4 50 mM K2SO4 500 % v/v D2O 1 mM MgCl2缓冲液浓度20.0 mM
pH6.6添加剂Na2SO4 200.000 mM, K2SO4 50.000 mM, D2O 50.000 % v/v, MgCl2 1.000 mM
缓冲液说明pD = 7.0
纯度测定方法Crystalline, Hampton Research消光系数1.075
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2013-12-10储存 / 测量温度10.0 / 10.0
曝光时间—帧数20
波长0.12样品-探测器距离3.1
光源X-ray synchrotron探测器Pilatus 2M
机构 / 束线PETRA III / EMBL P12 · DESY; Hamburg, Germany
q 范围0.091 – 3.501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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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：416 个字段值
字段路径原始值
codeSASDAB6
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleCorrelation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra.
project.publication.titleCorrelation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra.
project.publication.author_listFranke D, Jeffries CM, Svergun DI
project.publication.journalNat Methods
project.publication.doi10.1038/nmeth.3358
project.publication.pmid25849637
project.publication.published_date2015 May
project.statusreleased
project.submitted_datenull
project.released_date2015-05-01
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDAB6.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDAB6.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAB6_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAB6_kratky_img.png
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sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDAB6.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_nameXylose Isomerase
experiment.sample.molecule[0].short_nameGI Glucose isomerase
experiment.sample.molecule[0].sequence>4E3V|PDBID|COMPLETE|SEQUENCE MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALD DTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKE AFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGK LFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAF RADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALD DTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKE AFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGK LFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAF RADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALD DTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKE AFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGK LFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAF RADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALD DTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKE AFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGK LFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAF RADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG
experiment.sample.molecule[0].organismStreptomyces rubiginosus
experiment.sample.molecule[0].uniprot_codenull
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationtetramer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequencenull
experiment.sample.molecule[0].mw43.2
experiment.sample.molecule[0].total_mw172.8
experiment.sample.molecule[0].number_molecules4
experiment.sample.molecule[0].complex_statenull
experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
experiment.sample.molecule[0].molecule_descriptionnull
experiment.sample.buffer.name20 mM HEPES 200 mM Na2SO4 50 mM K2SO4 500 % v/v D2O 1 mM MgCl2
experiment.sample.buffer.concentration_unitmM
experiment.sample.buffer.commentpD = 7.0
experiment.sample.buffer.additiveNa2SO4 200.000 mM, K2SO4 50.000 mM, D2O 50.000 % v/v, MgCl2 1.000 mM
experiment.sample.buffer.concentration20.0
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph6.6
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodCrystalline, Hampton Research
experiment.sample.nameXylose Isomerase
experiment.sample.ext_coefficient1.075
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_nameDaniel
experiment.contributor[0].contributor_surnameFranke
experiment.contributor[0].orcidnull
experiment.contributor[1].affiliation[0].short_nameEMBL-Hamburg
experiment.contributor[1].affiliation[0].addressNotkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany
experiment.contributor[1].affiliation[0].full_nameEuropean Molecular Biology Laboratory (EMBL) - Hamburg outstation
experiment.contributor[1].affiliation[0].webpagehttp://www.embl-hamburg.de/index.php
experiment.contributor[1].contributor_nameCy M
experiment.contributor[1].contributor_surnameJeffries
experiment.contributor[1].orcidnull
experiment.contributor[2].affiliation[0].short_nameEMBL-Hamburg
experiment.contributor[2].affiliation[0].addressNotkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany
experiment.contributor[2].affiliation[0].full_nameEuropean Molecular Biology Laboratory (EMBL) - Hamburg outstation
experiment.contributor[2].affiliation[0].webpagehttp://www.embl-hamburg.de/index.php
experiment.contributor[2].contributor_nameDmitri
experiment.contributor[2].contributor_surnameSvergun
experiment.contributor[2].orcidnull
experiment.concentration_methodA280 nm
experiment.concentration_unitnull
experiment.date2013-12-10
experiment.storage_temperature10.0
experiment.cell_temperature10.0
experiment.exposure_timenull
experiment.number_of_frames20
experiment.wavelength0.12
experiment.sample_detector_distance3.1
experiment.concentration_minnull
experiment.concentration_max5.76
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.091
experiment.s_max3.501
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDAB6_fit1_model1_img.png
fits[0].models[0].softwareDAMMIF
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modeldummy
fits[0].models[0].software_version
fits[0].models[0].model_datahttps://www.sasbdb.org/media/pdb_file/SASDAB6_fit1_model1.pdb
fits[0].models[0].model_mw140.5
fits[0].models[0].bead_radius1.9
fits[0].models[0].loghttps://www.sasbdb.org/media/log_files/6.log
fits[0].models[0].symmetryP4
fits[0].models[0].comment
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i0_calibration_standardBSA
descriptionThe data displayed at the top of the entry, and the subsequent ab inito and atomic model fit, are data derived from averaging 20 individual frames. The individual 20 data frames used for the averaging are also displayed, with the respective atomic-model fits (CRYSOL; PDB 4E3V).
experiment_descriptionX-ray synchrotron radiation scattering data from solutions of Xylose Isomerase in 20 mM HEPES, 200 mM Na2SO4, 50 mM K2SO4, 50% v/v D2O, 1 mM MgCl2 mM, pH 6.6 were collected on the P12 beam line at Petra-III (Hamburg, Germany) using a Pilatus 2M detector (I(s) vs s, where s = 4π sin θ/λ; 2θ is the scattering angle and λ = 0.12 nm). One solute concentration at 5.76 mg/ml was measured using a total exposure time of 1 second (20 x 0.050 second frames). The data were normalized to the intensity of the transmitted beam and radially averaged. Scattering contributions from the matched solvent blank were subtracted and the resulting 1D scattering data were scaled to protein concentration. The data presented in this entry were obtained from a single concentration scattering curve.
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intensities_log_log_plotSASDAB6_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
codeSASDAB6
statussuccess
started_at2026-08-11T15:05:27.704952+00:00
finished_at2026-08-11T15:05:38.948789+00:00
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查看完整 summary.json 原文
{
  "code": "SASDAB6",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Correlation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra.",
    "publication": {
      "title": "Correlation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra.",
      "author_list": "Franke D, Jeffries CM, Svergun DI",
      "journal": "Nat Methods",
      "doi": "10.1038/nmeth.3358",
      "pmid": "25849637",
      "published_date": "2015 May"
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    "status": "released",
    "submitted_date": null,
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      "city": "DESY; Hamburg",
      "country": "Germany",
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查看完整 manifest.json 原文
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