SASDD43

Mycobacterial suicide toxin (MbsT)

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
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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Mycobacterial suicide toxin (MbsT)

浓度0.4 – 7.4 缓冲液 / pH30 mM Tris-HCl, 200 mM NaCl, 10% glycerol / 7.5
实验温度20.3 设备 / 束线PETRA III / EMBL P12
波长0.124 nm曝光0.05 s × 20

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
Mycobacterial cidal toxin
查看序列
>MBSTMDSDALDEGLVQRIDARGTIEWSETCYRYTGAHRDALSGEGARRFGGRWNPPLLFPAIYLADSAQACMVEVERAAQAASTTAEKMLEAAYRLHTIDVTDLAVLDLTTPQAREAVGLENDDIYGDDWSGCQAVGHAAWFLHMQGVLVPAAGGVGLVVTAYEQRTRPGQLQLRQSVDLTPALYQELRAT
proteinMycobacterium tuberculosis H37RvP9WLP91–186monomer分子数 120.396 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
11720[3]0.107882–4.83472 1/nm含误差列缺失 00sasbdb/entries/43/sasdd43/source/SASDD43.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)5.6—nm
i0Guinier18612.121.0arbitrary
i0P(r)18610.014.0arbitrary
mwExperimental18.0—kDa
mwGuinier I(0)18.02.0kDa
mwPorod17.0—kDa
porod_volumePorod30.0—nm³
rgGuinier1.750.1nm
rgP(r)1.7470.002nm

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30 mM Tris-HCl, 200 mM NaCl, 10% glycerol缓冲液浓度—
pH7.5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2017-05-02储存 / 测量温度20.0 / 20.3
曝光时间0.05帧数20
波长0.124样品-探测器距离2.0
光源X-ray synchrotron探测器Pilatus 2M
机构 / 束线PETRA III / EMBL P12 · DESY; Hamburg, Germany
q 范围0.108 – 4.835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/43/sasdd43/source/SASDD43.zipdownloaded20824626c6cdee899b7a28dd90ed424db4ae300c8cee25582b92b705b59db45bdcd546下载查看原文件源站
pddfsasbdb/entries/43/sasdd43/source/SASDD43.outdownloaded144704018d685de9e3b7ef010b94672ccbd6952c1f7da3e7ab4eb3d2d04356357d0365下载查看原文件源站
sascifsasbdb/entries/43/sasdd43/source/SASDD43.sascifdownloaded652601242be65607b27785f7812ad94864080e18c1dc99e990d6cd126461cf0d854220下载查看原文件源站
summarysasbdb/entries/43/sasdd43/source/summary.jsondownloaded826120fbdcc2fa6b5d9f627e6300ebfc3571c021cedc5d45ca6ba45c3f66894f0ba8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:177 个字段值
字段路径原始值
codeSASDD43
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleMbsTA
project.publicationnull
project.statusreleased
project.submitted_date2018-01-16
project.released_date2019-12-02
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sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDD43.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_nameMycobacterial cidal toxin
experiment.sample.molecule[0].short_nameMbcT
experiment.sample.molecule[0].sequence>MbsT MDSDALDEGLVQRIDARGTIEWSETCYRYTGAHRDALSGEGARRFGGRWNPPLLFPAIYLADSAQACMVEVERAAQAASTTAEKMLEAAYRLHTIDVTDLAVLDLTTPQAREAVGLENDDIYGDDWSGCQAVGHAAWFLHMQGVLVPAAGGVGLVVTAYEQRTRPGQLQLRQSVDLTPALYQELRAT
experiment.sample.molecule[0].organismMycobacterium tuberculosis H37Rv
experiment.sample.molecule[0].uniprot_codeP9WLP9
experiment.sample.molecule[0].uniprot_range_first1
experiment.sample.molecule[0].uniprot_range_last186
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMSDALDEGLVQRIDARGTIEWSETCYRYTGAHRDALSGEGARRFGGRWNPPLLFPAIYLA DSAQACMVEVERAAQAASTTAEKMLEAAYRLHTIDVTDLAVLDLTTPQAREAVGLENDDI YGDDWSGCQAVGHAAWFLHMQGVLVPAAGGVGLVVTAYEQRTRPGQLQLRQSVDLTPALY QELRAT
experiment.sample.molecule[0].mw20.396
experiment.sample.molecule[0].total_mw20.396
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.name30 mM Tris-HCl, 200 mM NaCl, 10% glycerol
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.5
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameMycobacterial suicide toxin (MbsT)
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_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_nameDiana
experiment.contributor[0].contributor_surnameFreire
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2017-05-02
experiment.storage_temperature20.0
experiment.cell_temperature20.3
experiment.exposure_time0.05
experiment.number_of_frames20
experiment.wavelength0.124
experiment.sample_detector_distance2.0
experiment.concentration_min0.4
experiment.concentration_max7.4
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.108
experiment.s_max4.835
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].bead_radius1.9
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fits[0].models[0].commentnull
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fits[0].softwareSREFLEX
fits[0].chi_square_value1.221
fits[0].p_value0.569452
fits[0].fit_residual_plotSASDD43_fit1_fitresiduals_img.png
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fits[0].fit_lognull
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fits[0].descriptionnull
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fits[1].models[0].softwarePDB (Protein Data Bank)
fits[1].models[0].pdb_link[0].pdb_code6fkg
fits[1].models[0].pdb_link[0].ext_code6FKG
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fits[1].models[0].software_versionnull
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fits[1].models[0].model_mw20.21
fits[1].models[0].bead_radius1.9
fits[1].models[0].lognull
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fits[1].models[0].commentnull
fits[1].models[0].user277
fits[1].fit_unit1/A
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fits[1].softwareCRYSOL
fits[1].chi_square_value2.204
fits[1].p_value0.0
fits[1].fit_residual_plotSASDD43_fit2_fitresiduals_img.png
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fits[1].fit_loghttps://www.sasbdb.org/media/fitting_files/log_files/MbsT_crysol.log
fits[1].software_versionnull
fits[1].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of Mycobacterial suicide toxin (MbsT) in 30 mM Tris-HCl, 200 mM NaCl, 10% glycerol, pH 7.5, were collected on the P12 beam line at the PETRA III storage ring (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 2 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Solute concentrations ranging between 0.4 and 7.4 mg/ml were measured at 20.3°C. 20 successive 0.050 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.
tags[]
intensity_unitarbitrary
experimental_mw18.0
experimental_mw_errornull
guinier_i0_mw18.0
guinier_i0_mw_error2.0
porod_mw17.0
porod_mw_errornull
pddf_i018610.0
pddf_i0_error14.0
guinier_i018612.1
guinier_i0_error21.0
pddf_rg1.747
pddf_rg_error0.002
guinier_rg1.75
guinier_rg_error0.1
pddf_dmax5.6
pddf_dmax_errornull
porod_volume30.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first1
guinier_point_last231
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDD43_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
codeSASDD43
statussuccess
started_at2026-08-11T13:51:53.022061+00:00
finished_at2026-08-11T13:52:08.906129+00:00
source_last_modified2023-06-21T07:56:39.492710+02:00
files[0].statusdownloaded
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查看完整 summary.json 原文
{
  "code": "SASDD43",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "MbsTA",
    "publication": null,
    "status": "released",
    "submitted_date": "2018-01-16",
    "released_date": "2019-12-02"
  },
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  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDD43.dat",
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  "experiment": {
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        "name": "Pilatus 2M",
        "resolution": null
      },
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      "city": "DESY; Hamburg",
      "country": "Germany",
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      "type_of_source": "X-ray synchrotron",
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      "xray_energy": null,
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    },
    "sample": {
      "molecule": [
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          "long_name": "Mycobacterial cidal toxin",
          "short_name": "MbcT",
          "sequence": ">MbsT\r\nMDSDALDEGLVQRIDARGTIEWSETCYRYTGAHRDALSGEGARRFGGRWNPPLLFPAIYLADSAQACMVEVERAAQAASTTAEKMLEAAYRLHTIDVTDLAVLDLTTPQAREAVGLENDDIYGDDWSGCQAVGHAAWFLHMQGVLVPAAGGVGLVVTAYEQRTRPGQLQLRQSVDLTPALYQELRAT",
          "organism": "Mycobacterium tuberculosis H37Rv",
          "uniprot_code": "P9WLP9",
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          "uniprot_range_last": 186,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MSDALDEGLVQRIDARGTIEWSETCYRYTGAHRDALSGEGARRFGGRWNPPLLFPAIYLA\nDSAQACMVEVERAAQAASTTAEKMLEAAYRLHTIDVTDLAVLDLTTPQAREAVGLENDDI\nYGDDWSGCQAVGHAAWFLHMQGVLVPAAGGVGLVVTAYEQRTRPGQLQLRQSVDLTPALY\nQELRAT",
          "mw": 20.396,
          "total_mw": 20.396,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
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查看完整 manifest.json 原文
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