SASDEA6

Staphylococcus aureus N-acetylglucosamine-6-phosphate deacetylase dimer

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Single concentration 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 · Staphylococcus aureus N-acetylglucosamine-6-phosphate deacetylase dimer

浓度— – 6.0 缓冲液 / pH20 mM Tris-HCl 150 mM NaCl / 8.0
实验温度20.0 设备 / 束线Australian Synchrotron / SAXS/WAXS
波长0.10332 nm曝光1.0 s × 999

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
N-acetylglucosamine-6-phosphate deacetylase
查看序列
>TR|A0A0H2XGG9|A0A0H2XGG9_STAA3N-ACETYLGLUCOSAMINE-6-PHOSPHATEDEACETYLASEOS=STAPHYLOCOCCUSAUREUS(STRAINUSA300)OX=367830GN=NAGAPE=3SV=1MSELIIYNGKVYTEDGKIDNGYIHVKDGQIVAIGEVDDKAAIDNDTTNKIQVIDAKGHHVLPGFIDIHIHGGYGQDAMDGSYDGLKYLSENLLSEGTTSYLATTMTQSTDKIDNALTNIAKYEAEQDVHNAAEIVGIHLEGPFISENKVGAQHPQYVVRPFIDKIKHFQETANGLIKIMTFAPEVEGAKEALETYKDDIIFSIGHTVATYEEAVEAVERGAKHVTHLYNAATPFQHREPGVFGAAWLNDALHTEMIVDGTHSHPASVAIAYRMKGNERFYLITDAMRAKGMPEGEYDLGGQKVTVQSQQARLANGALAGSILKMNHGLRNLISFTGDTLDHLWRVTSLNQAIALGIDDRKGSIKVNKDADLVILDDDMNVKSTIKQGKVHTFS
proteinStaphylococcus aureusA0A0H2XGG9—–—dimer分子数 243.115 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
1925[3]0.012102842–0.68656129 1/A含误差列缺失 05sasbdb/entries/a6/sasdea6/source/SASDEA6.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)10.1—Å
i0Guinier0.0549220.0002arbitrary
i0P(r)0.05517—arbitrary
mwExperimental82.1—kDa
mwPorod67.0—kDa
porod_volumePorod107.0—ų
rgGuinier3.1580.008Å
rgP(r)3.19—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 Tris-HCl 150 mM NaCl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2016-04-26储存 / 测量温度4.0 / 20.0
曝光时间1.0帧数999
波长0.10332样品-探测器距离1.6
光源X-ray synchrotron探测器Pilatus 1M
机构 / 束线Australian Synchrotron / SAXS/WAXS · Melbourne, Australia
q 范围0.121 – 6.866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/a6/sasdea6/source/SASDEA6.zipdownloaded1713022f21b847ad68b68c5b574b405291028ab7e427645061c9030d5b6e90936e8b10下载查看原文件源站
pddfsasbdb/entries/a6/sasdea6/source/SASDEA6.outdownloaded34108b1f6afe6f512975df12e32905eaa820dbfe80c379f46ee3636e8dce5fa5de4d6下载查看原文件源站
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summarysasbdb/entries/a6/sasdea6/source/summary.jsondownloaded8363c617ca4c0701ad2dd032e71bc2e6ecb852f670dbc4f82566724b5496a75be1a9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
codeSASDEA6
statusPublished
type_of_curveSingle concentration
angular_unit1/A
project.titleFunctional and solution structure studies of amino sugar deacetylase and deaminase enzymes from Staphylococcus aureus.
project.publication.titleFunctional and solution structure studies of amino sugar deacetylase and deaminase enzymes from Staphylococcus aureus.
project.publication.author_listDavies JS, Coombes D, Horne CR, Pearce FG, Friemann R, North RA, Dobson RCJ
project.publication.journalFEBS Lett
project.publication.doi10.1002/1873-3468.13289
project.publication.pmid30411345
project.publication.published_date2018 Nov 9
project.statusreleased
project.submitted_date2018-10-09
project.released_date2018-11-13
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intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDEA6.dat
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experiment.instrument.detector.typeDectris
experiment.instrument.detector.namePilatus 1M
experiment.instrument.detector.resolution172.0
experiment.instrument.nameAustralian Synchrotron
experiment.instrument.cityMelbourne
experiment.instrument.countryAustralia
experiment.instrument.beamline_nameSAXS/WAXS
experiment.instrument.beam_geometryPoint
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourceTrue
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_nameN-acetylglucosamine-6-phosphate deacetylase
experiment.sample.molecule[0].short_nameNagA
experiment.sample.molecule[0].sequence>tr|A0A0H2XGG9|A0A0H2XGG9_STAA3 N-acetylglucosamine-6-phosphate deacetylase OS=Staphylococcus aureus (strain USA300) OX=367830 GN=nagA PE=3 SV=1 MSELIIYNGKVYTEDGKIDNGYIHVKDGQIVAIGEVDDKAAIDNDTTNKIQVIDAKGHHV LPGFIDIHIHGGYGQDAMDGSYDGLKYLSENLLSEGTTSYLATTMTQSTDKIDNALTNIA KYEAEQDVHNAAEIVGIHLEGPFISENKVGAQHPQYVVRPFIDKIKHFQETANGLIKIMT FAPEVEGAKEALETYKDDIIFSIGHTVATYEEAVEAVERGAKHVTHLYNAATPFQHREPG VFGAAWLNDALHTEMIVDGTHSHPASVAIAYRMKGNERFYLITDAMRAKGMPEGEYDLGG QKVTVQSQQARLANGALAGSILKMNHGLRNLISFTGDTLDHLWRVTSLNQAIALGIDDRK GSIKVNKDADLVILDDDMNVKSTIKQGKVHTFS
experiment.sample.molecule[0].organismStaphylococcus aureus
experiment.sample.molecule[0].uniprot_codeA0A0H2XGG9
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMSELIIYNGKVYTEDGKIDNGYIHVKDGQIVAIGEVDDKAAIDNDTTNKIQVIDAKGHHV LPGFIDIHIHGGYGQDAMDGSYDGLKYLSENLLSEGTTSYLATTMTQSTDKIDNALTNIA KYEAEQDVHNAAEIVGIHLEGPFISENKVGAQHPQYVVRPFIDKIKHFQETANGLIKIMT FAPEVEGAKEALETYKDDIIFSIGHTVATYEEAVEAVERGAKHVTHLYNAATPFQHREPG VFGAAWLNDALHTEMIVDGTHSHPASVAIAYRMKGNERFYLITDAMRAKGMPEGEYDLGG QKVTVQSQQARLANGALAGSILKMNHGLRNLISFTGDTLDHLWRVTSLNQAIALGIDDRK GSIKVNKDADLVILDDDMNVKSTIKQGKVHTFS
experiment.sample.molecule[0].mw43.115
experiment.sample.molecule[0].total_mw86.23
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.name20 mM Tris-HCl 150 mM NaCl
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.nameStaphylococcus aureus N-acetylglucosamine-6-phosphate deacetylase dimer
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].addressNew Zealand
experiment.contributor[0].affiliation[0].full_nameUniversity of Canterbury
experiment.contributor[0].affiliation[0].webpagehttps://www.canterbury.ac.nz/
experiment.contributor[0].contributor_nameJames
experiment.contributor[0].contributor_surnameDavies
experiment.contributor[0].orcidhttps://orcid.org/0000-0003-4029-1650
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2016-04-26
experiment.storage_temperature4.0
experiment.cell_temperature20.0
experiment.exposure_time1.0
experiment.number_of_frames999
experiment.wavelength0.10332
experiment.sample_detector_distance1.6
experiment.concentration_minnull
experiment.concentration_max6.0
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.121
experiment.s_max6.866
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDEA6_fit1_model1_img.png
fits[0].models[0].softwarePyMOL
fits[0].models[0].pdb_link[0].pdb_code2vhl
fits[0].models[0].pdb_link[0].ext_code2VHL
fits[0].models[0].pdb_link[0].ext_typepdb
fits[0].models[0].pdb_link[0].difference_with_modelderived
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modelatomic
fits[0].models[0].software_version2.0.6
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fits[0].models[0].model_mw85.33
fits[0].models[0].bead_radiusnull
fits[0].models[0].lognull
fits[0].models[0].symmetrynull
fits[0].models[0].commentStructure of NagA isozyme from B subtilis fit to data. Generated using symmetry mates.
fits[0].models[0].user378
fits[0].fit_unit1/A
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fits[0].softwareCRYSOL
fits[0].chi_square_value0.207
fits[0].p_value0.0
fits[0].fit_residual_plot2vhl_dimer_5nSEn9j_fitresiduals_img.png
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fits[0].software_versionATSAS 2.8
fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of Staphylococcus aureus N-acetylglucosamine-6-phosphate deacetylase dimer in 20 mM Tris-HCl, 150 mM NaCl, pH 8 were collected on the SAXS/WAXS beam line at the Australian Synchrotron (Melbourne, Australia) using a Pilatus 1M detector at a sample-detector distance of 1.6 m and at a wavelength of λ = 0.10332 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 6.00 mg/ml was measured at 20°C. 999 successive 1 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_mw82.1
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw67.0
porod_mw_errornull
pddf_i00.05517
pddf_i0_errornull
guinier_i00.054922
guinier_i0_error0.0002
pddf_rg3.19
pddf_rg_errornull
guinier_rg3.158
guinier_rg_error0.008
pddf_dmax10.1
pddf_dmax_errornull
porod_volume107.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first9
guinier_point_last40
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDEA6_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
codeSASDEA6
statussuccess
started_at2026-08-11T15:04:56.132419+00:00
finished_at2026-08-11T15:05:06.208319+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": "SASDEA6",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/A",
  "project": {
    "title": "Functional and solution structure studies of amino sugar deacetylase and deaminase enzymes from Staphylococcus aureus.",
    "publication": {
      "title": "Functional and solution structure studies of amino sugar deacetylase and deaminase enzymes from Staphylococcus aureus.",
      "author_list": "Davies JS, Coombes D, Horne CR, Pearce FG, Friemann R, North RA, Dobson RCJ",
      "journal": "FEBS Lett",
      "doi": "10.1002/1873-3468.13289",
      "pmid": "30411345",
      "published_date": "2018 Nov 9"
    },
    "status": "released",
    "submitted_date": "2018-10-09",
    "released_date": "2018-11-13"
  },
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      "country": "Australia",
      "beamline_name": "SAXS/WAXS",
      "beam_geometry": "Point",
      "type_of_source": "X-ray synchrotron",
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          "long_name": "N-acetylglucosamine-6-phosphate deacetylase",
          "short_name": "NagA",
          "sequence": ">tr|A0A0H2XGG9|A0A0H2XGG9_STAA3 N-acetylglucosamine-6-phosphate deacetylase OS=Staphylococcus aureus (strain USA300) OX=367830 GN=nagA PE=3 SV=1\r\nMSELIIYNGKVYTEDGKIDNGYIHVKDGQIVAIGEVDDKAAIDNDTTNKIQVIDAKGHHV\r\nLPGFIDIHIHGGYGQDAMDGSYDGLKYLSENLLSEGTTSYLATTMTQSTDKIDNALTNIA\r\nKYEAEQDVHNAAEIVGIHLEGPFISENKVGAQHPQYVVRPFIDKIKHFQETANGLIKIMT\r\nFAPEVEGAKEALETYKDDIIFSIGHTVATYEEAVEAVERGAKHVTHLYNAATPFQHREPG\r\nVFGAAWLNDALHTEMIVDGTHSHPASVAIAYRMKGNERFYLITDAMRAKGMPEGEYDLGG\r\nQKVTVQSQQARLANGALAGSILKMNHGLRNLISFTGDTLDHLWRVTSLNQAIALGIDDRK\r\nGSIKVNKDADLVILDDDMNVKSTIKQGKVHTFS",
          "organism": "Staphylococcus aureus",
          "uniprot_code": "A0A0H2XGG9",
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "dimer",
          "molecular_type": "protein",
          "uniprot_sequence": "MSELIIYNGKVYTEDGKIDNGYIHVKDGQIVAIGEVDDKAAIDNDTTNKIQVIDAKGHHV\nLPGFIDIHIHGGYGQDAMDGSYDGLKYLSENLLSEGTTSYLATTMTQSTDKIDNALTNIA\nKYEAEQDVHNAAEIVGIHLEGPFISENKVGAQHPQYVVRPFIDKIKHFQETANGLIKIMT\nFAPEVEGAKEALETYKDDIIFSIGHTVATYEEAVEAVERGAKHVTHLYNAATPFQHREPG\nVFGAAWLNDALHTEMIVDGTHSHPASVAIAYRMKGNERFYLITDAMRAKGMPEGEYDLGG\nQKVTVQSQQARLANGALAGSILKMNHGLRNLISFTGDTLDHLWRVTSLNQAIALGIDDRK\nGSIKVNKDADLVILDDDMNVKSTIKQGKVHTFS",
          "mw": 43.115,
          "total_mw": 86.23,
          "number_molecules": 2,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "20 mM Tris-HCl 150 mM NaCl",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 8.0,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Staphylococcus aureus N-acetylglucosamine-6-phosphate deacetylase dimer",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "New Zealand",
            "full_name": "University of Canterbury",
            "webpage": "https://www.canterbury.ac.nz/"
          }
        ],
        "contributor_name": "James",
        "contributor_surname": "Davies",
        "orcid": "https://orcid.org/0000-0003-4029-1650"
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2016-04-26",
    "storage_temperature": 4.0,
    "cell_temperature": 20.0,
    "exposure_time": 1.0,
    "number_of_frames": 999,
    "wavelength": 0.10332,
    "sample_detector_distance": 1.6,
    "concentration_min": null,
    "concentration_max": 6.0,
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    "s_min": 0.121,
    "s_max": 6.866,
    "total_exposure_time": null,
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          "software": "PyMOL",
          "pdb_link": [
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              "ext_code": "2VHL",
              "ext_type": "pdb",
              "difference_with_model": "derived"
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          "comment": "Structure of NagA isozyme from B subtilis fit to data. Generated using symmetry mates.",
          "user": 378
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      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/2vhl_dimer_5nSEn9j_fit_img.png",
      "software": "CRYSOL",
      "chi_square_value": 0.207,
      "p_value": 0.0,
      "fit_residual_plot": "2vhl_dimer_5nSEn9j_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEA6_fit1.fit",
      "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/2vhl_dimer_MpnFcww.log",
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      "description": ""
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  "description": null,
  "experiment_description": "Synchrotron SAXS data from solutions of Staphylococcus aureus N-acetylglucosamine-6-phosphate deacetylase dimer in 20 mM Tris-HCl, 150 mM NaCl, pH 8 were collected on the SAXS/WAXS beam line at the Australian Synchrotron (Melbourne, Australia) using a Pilatus 1M detector at a sample-detector distance of 1.6 m and at a wavelength of λ = 0.10332 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 6.00 mg/ml was measured at 20°C. 999 successive 1 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.",
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  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDEA6_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
  "bragg_peak": []
}
查看完整 manifest.json 原文
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