SASDFG7

Pseudomonas putida CBB5 NdmB hexamer

数据类型:SASBDB 实验数据 状态:Published 曲线类型:SEC-SAS 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 · Pseudomonas putida CBB5 NdmB hexamer

浓度— – 9.7 缓冲液 / pH20 mM HEPES 150 mM NaCl 2 mM TCEP / 7.5
实验温度18.0 设备 / 束线Photon Factory (PF), High Energy Accelerator Research Organization (KEK) / BL-10C
波长0.15 nm曝光10.0 s × 36

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
Methylxanthine N3-demethylase NdmB
查看序列
MGSSHHHHHHENLYFQGSMKEQLKPLLEDKTYLRHFWHPVCTLNEFERANASGHGPMGVTLLGEKLVLARLNSKIIAAADRCAHRSAQLSIGRVCSNAGKDYLECPYHGWRYDEAGACQLIPACPDKSISPRAKISSFDCEVKYDIVWVRLDNSFDCTQIPYLSDFDNPDMQVIVADSYIWETVAERRWENFTDFSHFAFVHPGTLYDPFFASHPTVYVNRVDGELQFKLAPPREMKGIPPEAPMGDFTYRCTMPYSVNLEIKLWKDDSRFVLWTTASPVDNKSCRNFMIIVREKDNQPDHMHLAFQKRVLDEDQPVIESQWPLEIQTSEVSVATDKISVQFRKWHKELSLSAVEGREAFRDSVLTNVIEEEQ
proteinPseudomonas putidaH9N290—–—hexamer分子数 643.012 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
11170[3]0.003329395–0.2808594 1/A含误差列缺失 0227sasbdb/entries/g7/sasdfg7/source/SASDFG7.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)12.23—Å
i0Guinier0.61—1/cm
i0P(r)0.6081—1/cm
mwExperimental275.0—kDa
rgGuinier4.325—Å
rgP(r)4.24—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

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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 150 mM NaCl 2 mM TCEP缓冲液浓度—
pH7.5添加剂—
缓冲液说明gel filtration buffer
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2018-05-21储存 / 测量温度4.0 / 18.0
曝光时间10.0帧数36
波长0.15样品-探测器距离3.0
光源X-ray synchrotron探测器Pilatus3 2M
机构 / 束线Photon Factory (PF), High Energy Accelerator Research Organization (KEK) / BL-10C · Tsukuba, Japan
q 范围0.033 – 2.809样品体积 / 流速140.0 / 0.05

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
codeSASDFG7
statusPublished
type_of_curveSEC-SAS
angular_unit1/A
project.titleStructural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex.
project.publication.titleStructural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex.
project.publication.author_listKim JH, Kim BH, Brooks S, Kang SY, Summers RM, Song HK
project.publication.journalJ Mol Biol
project.publication.doi10.1016/j.jmb.2019.08.004
project.publication.pmid31412262
project.publication.published_date2019 Sep 6
project.statusreleased
project.submitted_date2019-06-17
project.released_date2019-09-16
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDFG7.out
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experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus3 2M
experiment.instrument.detector.resolution0.172
experiment.instrument.namePhoton Factory (PF), High Energy Accelerator Research Organization (KEK)
experiment.instrument.cityTsukuba
experiment.instrument.countryJapan
experiment.instrument.beamline_nameBL-10C
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_nameMethylxanthine N3-demethylase NdmB
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceMGSSHHHHHHENLYFQGSMKEQLKPLLEDKTYLRHFWHPVCTLNEFERANASGHGPMGVTLLGEKLVLARLNSKIIAA ADRCAHRSAQLSIGRVCSNAGKDYLECPYHGWRYDEAGACQLIPACPDKSISPRAKISSF DCEVKYDIVWVRLDNSFDCTQIPYLSDFDNPDMQVIVADSYIWETVAERRWENFTDFSHF AFVHPGTLYDPFFASHPTVYVNRVDGELQFKLAPPREMKGIPPEAPMGDFTYRCTMPYSV NLEIKLWKDDSRFVLWTTASPVDNKSCRNFMIIVREKDNQPDHMHLAFQKRVLDEDQPVI ESQWPLEIQTSEVSVATDKISVQFRKWHKELSLSAVEGREAFRDSVLTNVIEEEQ
experiment.sample.molecule[0].organismPseudomonas putida
experiment.sample.molecule[0].uniprot_codeH9N290
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_sequenceMKEQLKPLLEDKTYLRHFWHPVCTLNEFERANASGHGPMGVTLLGEKLVLARLNSKIIAA ADRCAHRSAQLSIGRVCSNAGKDYLECPYHGWRYDEAGACQLIPACPDKSISPRAKISSF DCEVKYDIVWVRLDNSFDCTQIPYLSDFDNPDMQVIVADSYIWETVAERRWENFTDFSHF AFVHPGTLYDPFFASHPTVYVNRVDGELQFKLAPPREMKGIPPEAPMGDFTYRCTMPYSV NLEIKLWKDDSRFVLWTTASPVDNKSCRNFMIIVREKDNQPDHMHLAFQKRVLDEDQPVI ESQWPLEIQTSEVSVATDKISVQFRKWHKELSLSAVEGREAFRDSVLTNVIEEEQ
experiment.sample.molecule[0].mw43.012
experiment.sample.molecule[0].total_mw258.072
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 HEPES 150 mM NaCl 2 mM TCEP
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentgel filtration buffer
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.namePseudomonas putida CBB5 NdmB hexamer
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].addressSouth Korea
experiment.contributor[0].affiliation[0].full_nameKorea University
experiment.contributor[0].affiliation[0].webpagehttps://www.korea.edu/
experiment.contributor[0].contributor_nameJun Hoe
experiment.contributor[0].contributor_surnameKim
experiment.contributor[0].orcidhttps://orcid.org/0000-0001-5866-9952
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2018-05-21
experiment.storage_temperature4.0
experiment.cell_temperature18.0
experiment.exposure_time10.0
experiment.number_of_frames36
experiment.wavelength0.15
experiment.sample_detector_distance3.0
experiment.concentration_minnull
experiment.concentration_max9.7
experiment.sample_volume140.0
experiment.flow_rate0.05
experiment.s_min0.033
experiment.s_max2.809
experiment.total_exposure_timenull
experiment.seccolumn1
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDFG7_fit1_model1_img.png
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fits[0].models[0].bead_radius4.0
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fits[0].models[0].symmetryP3
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fits[0].p_value0.294224
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fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionnull
tags[]
intensity_unit1/cm
experimental_mw275.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i00.6081
pddf_i0_errornull
guinier_i00.61
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pddf_rg4.24
pddf_rg_errornull
guinier_rg4.325
guinier_rg_errornull
pddf_dmax12.23
pddf_dmax_errornull
porod_volumenull
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first12
guinier_point_last113
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDFG7_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
codeSASDFG7
statussuccess
started_at2026-08-11T15:29:21.285823+00:00
finished_at2026-08-11T15:29:34.354155+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": "SASDFG7",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/A",
  "project": {
    "title": "Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex.",
    "publication": {
      "title": "Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex.",
      "author_list": "Kim JH, Kim BH, Brooks S, Kang SY, Summers RM, Song HK",
      "journal": "J Mol Biol",
      "doi": "10.1016/j.jmb.2019.08.004",
      "pmid": "31412262",
      "published_date": "2019 Sep 6"
    },
    "status": "released",
    "submitted_date": "2019-06-17",
    "released_date": "2019-09-16"
  },
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      "country": "Japan",
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    "sample": {
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        {
          "long_name": "Methylxanthine N3-demethylase NdmB",
          "short_name": null,
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          "organism": "Pseudomonas putida",
          "uniprot_code": "H9N290",
          "uniprot_range_first": null,
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          "oligomerization": "hexamer",
          "molecular_type": "protein",
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          "mw": 43.012,
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查看完整 manifest.json 原文
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