SASDBK9

Geobacillus stearothermophilus DnaB full-length

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Merged 最后更新:2021-12-03T19:22:21.480997+01:00
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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Geobacillus stearothermophilus DnaB full-length

浓度2.0 – 10.0 缓冲液 / pH20 mM Tris, 300 mM NaCl and 5 mM β-ME / 8.0
实验温度15.0 设备 / 束线Taiwan Photon Source, NSRRC / 23A
波长0.08285 nm曝光30.0 s × 10

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
Geobacillus stearothermophilus DnaB full-length
查看序列
MQHHWKELIAVDRYTVQSRGVLQEVDRKVLTLLYQPLIGCRALALYMTLWGELELLDGQEATHHRLMALMQCGLPDIYSERLKLEGIGLLDTYVHAKEADEPKLFLYELRPPLAPDQFFRDEMLSVFLRRQVGRHLFIQLSNFFARPSIDETKFTQVTRSFSDVFSAVPAEQIVAGLSEEAGPELLEGKDHIRRDEASYVLDDGVFDFELFFAGLSKQLVPRRAVTAKVKEAIKKLAFLYGIPPLEMQKLVLGVIDPAYHIDIDALRRAAREWYELEHGGVEPRLVERVQPLAYRTMENIEPRTKEEQLMKQLETISPRQLLKEISGGAEPSLADLQLIEDVMFKQQLLPGVVNVLIYYVMLRTNMKLSKKYVEKIASHWARKKVKTVKEAMELAKEEAKTYQNWANEKEKGTRTVRKVVRTEIVPDWLNMDYSQPDDDDFDVEQARKELEERLKKYRDES
proteinGeobacillus stearothermophilusA0A0K2H6I1—–—tetramer分子数 453.494 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
1228[3]0.01123–0.33166 1/A含误差列缺失 00sasbdb/entries/k9/sasdbk9/source/SASDBK9.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)20.0—Å
i0Guinier0.191——
i0P(r)0.191——
mwExperimental53.526—kDa
mwGuinier I(0)199.135—kDa
porod_volumePorod431.66—ų
rgGuinier5.745—Å
rgP(r)5.7450.199Å

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 Tris, 300 mM NaCl and 5 mM β-ME缓冲液浓度—
pH8.0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2015-03-12储存 / 测量温度— / 15.0
曝光时间30.0帧数10
波长0.08285样品-探测器距离—
光源X-ray synchrotron探测器Flat Panel sensor C10158DK-3957(X)
机构 / 束线Taiwan Photon Source, NSRRC / 23A · Hsinchu, Taiwan
q 范围0.112 – 3.317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/k9/sasdbk9/source/SASDBK9.zipdownloaded73449f3d9389d1bc0d55aae62bfb0ad0eef0e09846da0cd16a90626535f25a420863b下载查看原文件源站
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summarysasbdb/entries/k9/sasdbk9/source/summary.jsondownloaded82420bb0e2069cd49af649c761abbd4d9ecac9c314ec4e17f3115d5a0d185801e8df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:156 个字段值
字段路径原始值
codeSASDBK9
statusPublished
type_of_curveMerged
angular_unit1/A
project.titleStructural analyses of the bacterial primosomal protein DnaB reveal that it is a tetramer and forms a complex with a primosomal re-initiation protein.
project.publication.titleStructural analyses of the bacterial primosomal protein DnaB reveal that it is a tetramer and forms a complex with a primosomal re-initiation protein.
project.publication.author_listLi YC, Naveen V, Lin MG, Hsiao CD
project.publication.journalJ Biol Chem
project.publication.doi10.1074/jbc.M117.792002
project.publication.pmid28808061
project.publication.published_date2017 Sep 22
project.statusreleased
project.submitted_date2017-01-04
project.released_date2018-01-23
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDBK9.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDBK9.dat
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experiment.instrument.detector.typenull
experiment.instrument.detector.nameFlat Panel sensor C10158DK-3957(X)
experiment.instrument.detector.resolution50.0
experiment.instrument.nameTaiwan Photon Source, NSRRC
experiment.instrument.cityHsinchu
experiment.instrument.countryTaiwan
experiment.instrument.beamline_name23A
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_nameGeobacillus stearothermophilus DnaB full-length
experiment.sample.molecule[0].short_nameGstDnaBFL
experiment.sample.molecule[0].sequenceMQHHWKELIAVDRYTVQSRGVLQEVDRKVLTLLYQPLIGCRALALYMTLWGELELLDGQEATHHRLMALM QCGLPDIYSERLKLEGIGLLDTYVHAKEADEPKLFLYELRPPLAPDQFFRDEMLSVFLRRQVGRHLFIQL SNFFARPSIDETKFTQVTRSFSDVFSAVPAEQIVAGLSEEAGPELLEGKDHIRRDEASYVLDDGVFDFEL FFAGLSKQLVPRRAVTAKVKEAIKKLAFLYGIPPLEMQKLVLGVIDPAYHIDIDALRRAAREWYELEHGG VEPRLVERVQPLAYRTMENIEPRTKEEQLMKQLETISPRQLLKEISGGAEPSLADLQLIEDVMFKQQLLP GVVNVLIYYVMLRTNMKLSKKYVEKIASHWARKKVKTVKEAMELAKEEAKTYQNWANEKEKGTRTVRKVV RTEIVPDWLNMDYSQPDDDDFDVEQARKELEERLKKYRDES
experiment.sample.molecule[0].organismGeobacillus stearothermophilus
experiment.sample.molecule[0].uniprot_codeA0A0K2H6I1
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_sequenceMQHHWKELIAVDRYTVQSRGVLQEVDRKVLTLLYQPLIGCRALALYMTLWGELELLDGQE ATHHRLMALMQCGLPDIYSERLKLEGIGLLDTYVHAKEADEPKLFLYELRPPLAPDQFFR DEMLSVFLRRQVGRHLFIQLSNFFARPSIDETKFTQVTRSFSDVFSAVPAEQIVAGLSEE AGPELLEGKDHIRRDEASYVLDDGVFDFELFFAGLSKQLVPRRAVTAKVKEAIKKLAFLY GIPPLEMQKLVLGVIDPAYHIDIDALRRAAREWYELEHGGVEPRLVERVQPLAYRTMENI EPRTKEEQLMKQLETISPRQLLKEISGGAEPSLADLQLIEDIMFQQQLLPGVVNVLIYYV MLRTNMKLSKKYVEKIASHWARKKVKTVKEAMELAKEEAKTYQNWANEKEKGTRTVRKVV RTEIVPDWLNMDYSQPDDDDFDVEQARKELEERLKKYRDES
experiment.sample.molecule[0].mw53.494
experiment.sample.molecule[0].total_mw213.976
experiment.sample.molecule[0].number_molecules4
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 Tris, 300 mM NaCl and 5 mM β-ME
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph8.0
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameGeobacillus stearothermophilus DnaB full-length
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].addressTaipei, Taiwan
experiment.contributor[0].affiliation[0].full_nameAcademia Sinica
experiment.contributor[0].affiliation[0].webpagehttps://www.sinica.edu.tw
experiment.contributor[0].contributor_nameYiChing
experiment.contributor[0].contributor_surnameLi
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2015-03-12
experiment.storage_temperaturenull
experiment.cell_temperature15.0
experiment.exposure_time30.0
experiment.number_of_frames10
experiment.wavelength0.08285
experiment.sample_detector_distancenull
experiment.concentration_min2.0
experiment.concentration_max10.0
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.112
experiment.s_max3.317
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDBK9_fit1_model1_img.png
fits[0].models[0].softwareGASBOR
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
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fits[0].models[0].software_version
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fits[0].models[0].model_mwnull
fits[0].models[0].bead_radius1.9
fits[0].models[0].lognull
fits[0].models[0].symmetry
fits[0].models[0].comment
fits[0].models[0].user194
fits[0].fit_unit1/A
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fits[0].softwareGASBOR
fits[0].chi_square_value1.43
fits[0].p_value0.000199
fits[0].fit_residual_plotSASDBK9_fit1_fitresiduals_img.png
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fits[0].software_version
fits[0].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionATSAS 2.6.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of Geobacillus stearothermophilus DnaB full-length in 20 mM Tris, 300 mM NaCl and 5 mM β-ME, pH 8 were collected on the 23A beam line at the Taiwan Photon Source storage ring (NSRRC, Hsinchu, Taiwan) using a Flat Panel sensor C10158DK-3957(X) detector at a wavelength of λ = 0.08285 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Solute concentrations ranging between 2 and 10 mg/ml were measured at 15°C. 10 successive 30 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 and the different curves were scaled for protein concentration. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.
tags[]
intensity_unitnull
experimental_mw53.526
experimental_mw_errornull
guinier_i0_mw199.135
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i00.191
pddf_i0_errornull
guinier_i00.191
guinier_i0_errornull
pddf_rg5.745
pddf_rg_error0.199
guinier_rg5.745
guinier_rg_errornull
pddf_dmax20.0
pddf_dmax_errornull
porod_volume431.66
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_firstnull
guinier_point_lastnull
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDBK9_datloglog_img.png
symmetrynull
last_modified2021-12-03T19:22:21.480997+01:00
bragg_peak[]
manifest.json:36 个字段值
字段路径原始值
codeSASDBK9
statussuccess
started_at2026-08-11T16:16:08.811604+00:00
finished_at2026-08-11T16:16:19.657850+00:00
source_last_modified2021-12-03T19:22:21.480997+01:00
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查看完整 summary.json 原文
{
  "code": "SASDBK9",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/A",
  "project": {
    "title": "Structural analyses of the bacterial primosomal protein DnaB reveal that it is a tetramer and forms a complex with a primosomal re-initiation protein.",
    "publication": {
      "title": "Structural analyses of the bacterial primosomal protein DnaB reveal that it is a tetramer and forms a complex with a primosomal re-initiation protein.",
      "author_list": "Li YC, Naveen V, Lin MG, Hsiao CD",
      "journal": "J Biol Chem",
      "doi": "10.1074/jbc.M117.792002",
      "pmid": "28808061",
      "published_date": "2017 Sep 22"
    },
    "status": "released",
    "submitted_date": "2017-01-04",
    "released_date": "2018-01-23"
  },
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      },
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      "type_of_source": "X-ray synchrotron",
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    },
    "sample": {
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          "long_name": "Geobacillus stearothermophilus DnaB full-length",
          "short_name": "GstDnaBFL",
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          "organism": "Geobacillus stearothermophilus",
          "uniprot_code": "A0A0K2H6I1",
          "uniprot_range_first": null,
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          "oligomerization": "tetramer",
          "molecular_type": "protein",
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          "number_molecules": 4,
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          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
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        "name": "20 mM Tris, 300 mM NaCl and 5 mM β-ME",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
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        "pka": null,
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        "deuteration": null
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      "purity_method": null,
      "name": "Geobacillus stearothermophilus DnaB full-length",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
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    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Taipei, Taiwan",
            "full_name": "Academia Sinica",
            "webpage": "https://www.sinica.edu.tw"
          }
        ],
        "contributor_name": "YiChing",
        "contributor_surname": "Li",
        "orcid": null
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    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2015-03-12",
    "storage_temperature": null,
    "cell_temperature": 15.0,
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          "comment": "",
          "user": 194
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      "software": "GASBOR",
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      "p_value": 0.000199,
      "fit_residual_plot": "SASDBK9_fit1_fitresiduals_img.png",
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  "description": null,
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  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDBK9_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2021-12-03T19:22:21.480997+01:00",
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}
查看完整 manifest.json 原文
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