SASDEM3

Dimeric class D beta-lactamase OXA-48

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Merged 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 · Dimeric class D beta-lactamase OXA-48

浓度0.1 – 13.0 缓冲液 / pH50 mM HEPES 50 mM K2SO4 / 7.0
实验温度25.0 设备 / 束线ESRF / BM29
波长0.09919 nm曝光10.0 s × 10

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
Beta-lactamase
查看序列
AKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP
proteinKlebsiella pneumoniaeQ6XEC022–265dimer分子数 228.218 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
11025[3]0.07883405–4.899328 1/nm含误差列缺失 00sasbdb/entries/m3/sasdem3/source/SASDEM3.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)7.35—nm
i0Guinier27.040.052arbitrary
i0P(r)26.79—arbitrary
mwExperimental50.0—kDa
mwPorod46.0—kDa
porod_volumePorod74.0—nm³
rgGuinier2.470.018nm
rgP(r)2.476—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50 mM HEPES 50 mM K2SO4缓冲液浓度—
pH7.0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2017-02-23储存 / 测量温度25.0 / 25.0
曝光时间10.0帧数10
波长0.09919样品-探测器距离2.867
光源X-ray synchrotron探测器Pilatus 1M
机构 / 束线ESRF / BM29 · Grenoble, France
q 范围0.079 – 4.899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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pddfsasbdb/entries/m3/sasdem3/source/SASDEM3.outdownloaded6236671a067b560ac7d6e0fe40bc68f5b1320fb71bc8e8e51edb22538804bd18bf06a下载查看原文件源站
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summarysasbdb/entries/m3/sasdem3/source/summary.jsondownloaded78144ba7901598ddaa0794a4278ffe84e183877ffa22bb2ecec5a18df53dcb2b5008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:159 个字段值
字段路径原始值
codeSASDEM3
statusPublished
type_of_curveMerged
angular_unit1/nm
project.titleThe biological assembly of OXA-48 reveals a dimer interface with high charge complementarity and very high affinity.
project.publication.titleThe biological assembly of OXA-48 reveals a dimer interface with high charge complementarity and very high affinity.
project.publication.author_listLund BA, Thomassen AM, Nesheim BHB, Carlsen TJO, Isaksson J, Christopeit T, Leiros HS
project.publication.journalFEBS J
project.publication.doi10.1111/febs.14643
project.publication.pmid30153368
project.publication.published_date2018 Aug 28
project.statusreleased
project.submitted_date2018-08-30
project.released_date2018-08-31
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experiment.instrument.detector.namePilatus 1M
experiment.instrument.detector.resolution172.0
experiment.instrument.nameESRF
experiment.instrument.cityGrenoble
experiment.instrument.countryFrance
experiment.instrument.beamline_nameBM29
experiment.instrument.beam_geometry
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourcenull
experiment.instrument.line_collimationnull
experiment.instrument.sample_path_lengthnull
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experiment.instrument.xray_energynull
experiment.instrument.beam_profile_ahnull
experiment.instrument.beam_profile_alnull
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experiment.sample.molecule[0].short_nameOXA-48
experiment.sample.molecule[0].sequenceAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALD LGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAF DYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGD YIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEK IIP
experiment.sample.molecule[0].organismKlebsiella pneumoniae
experiment.sample.molecule[0].uniprot_codeQ6XEC0
experiment.sample.molecule[0].uniprot_range_first22
experiment.sample.molecule[0].uniprot_range_last265
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
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experiment.sample.molecule[0].mw28.218
experiment.sample.molecule[0].total_mw56.436
experiment.sample.molecule[0].number_molecules2
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.name50 mM HEPES 50 mM K2SO4
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.0
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameDimeric class D beta-lactamase OXA-48
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_nameUiT
experiment.contributor[0].affiliation[0].addressTromso, Norway
experiment.contributor[0].affiliation[0].full_nameUiT - The Arctic University of Norway
experiment.contributor[0].affiliation[0].webpagehttps://en.uit.no/
experiment.contributor[0].contributor_nameBjarte Aarmo
experiment.contributor[0].contributor_surnameLund
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2017-02-23
experiment.storage_temperature25.0
experiment.cell_temperature25.0
experiment.exposure_time10.0
experiment.number_of_frames10
experiment.wavelength0.09919
experiment.sample_detector_distance2.867
experiment.concentration_min0.1
experiment.concentration_max13.0
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.079
experiment.s_max4.899
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].softwarePDB (Protein Data Bank)
fits[0].models[0].pdb_link[0].pdb_code5dtk
fits[0].models[0].pdb_link[0].ext_code5DTK
fits[0].models[0].pdb_link[0].ext_typepdb
fits[0].models[0].pdb_link[0].difference_with_modelderived
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fits[0].models[0].model_mw57.14
fits[0].models[0].bead_radius1.9
fits[0].models[0].lognull
fits[0].models[0].symmetry
fits[0].models[0].commentchains A and D
fits[0].models[0].user230
fits[0].fit_unit1/A
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fits[0].softwareCRYSOL
fits[0].chi_square_value5.025
fits[0].p_value0.0
fits[0].fit_residual_plot5dtk-A-D00_fitresiduals_img.png
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fits[0].software_version28
fits[0].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of dimeric class D beta-lactamase (OXA-48) in 50 mM HEPES, 50 mM K2SO4, pH 7, were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Dectris Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.09919 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.1 and 13 mg/ml were measured at 25°C. 10 successive 10 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The low angle data collected at lower concentration(s) were merged with the higher concentration high angle data to yield the final composite scattering curve.
tags[]
intensity_unitarbitrary
experimental_mw50.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw46.0
porod_mw_errornull
pddf_i026.79
pddf_i0_errornull
guinier_i027.04
guinier_i0_error0.052
pddf_rg2.476
pddf_rg_errornull
guinier_rg2.47
guinier_rg_error0.018
pddf_dmax7.35
pddf_dmax_errornull
porod_volume74.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first2
guinier_point_last96
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDEM3_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
codeSASDEM3
statussuccess
started_at2026-08-11T14:03:21.439443+00:00
finished_at2026-08-11T14:03:30.902934+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": "SASDEM3",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/nm",
  "project": {
    "title": "The biological assembly of OXA-48 reveals a dimer interface with high charge complementarity and very high affinity.",
    "publication": {
      "title": "The biological assembly of OXA-48 reveals a dimer interface with high charge complementarity and very high affinity.",
      "author_list": "Lund BA, Thomassen AM, Nesheim BHB, Carlsen TJO, Isaksson J, Christopeit T, Leiros HS",
      "journal": "FEBS J",
      "doi": "10.1111/febs.14643",
      "pmid": "30153368",
      "published_date": "2018 Aug 28"
    },
    "status": "released",
    "submitted_date": "2018-08-30",
    "released_date": "2018-08-31"
  },
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  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEM3.dat",
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        "name": "Pilatus 1M",
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      },
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      "country": "France",
      "beamline_name": "BM29",
      "beam_geometry": "",
      "type_of_source": "X-ray synchrotron",
      "point_source": null,
      "line_collimation": null,
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    },
    "sample": {
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          "long_name": "Beta-lactamase",
          "short_name": "OXA-48",
          "sequence": "AKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALD\r\nLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAF\r\nDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGD\r\nYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEK\r\nIIP",
          "organism": "Klebsiella pneumoniae",
          "uniprot_code": "Q6XEC0",
          "uniprot_range_first": 22,
          "uniprot_range_last": 265,
          "oligomerization": "dimer",
          "molecular_type": "protein",
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          "total_mw": 56.436,
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          "deuteration": null,
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          "molecule_description": null
        }
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查看完整 manifest.json 原文
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