SASDA89

Complex between ovine GM-CSF and GM-CSF/IL-2 inhibition factor

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Other 最后更新:2019-12-06T13:07:15.624532+01:00

Modeling of SAXS data: The crystal structure of the GIF:oGM-CSF complex was used as an input for the Allosmod-FoXS web server to model missing loops, N- and C-termini and N-linked glycosylation. During each Allosmod-FoXS run, data up to a scattering angle of 0.5 Å-1 was used. Fits to the experimental SAXS data were calculated using the FoXS software.

1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Complex between ovine GM-CSF and GM-CSF/IL-2 inhibition factor

浓度— – 9.7 mg/ml缓冲液 / pH20 mM HEPES 150 mM NaCl / 7.4
实验温度20.0 设备 / 束线SOLEIL / SWING
波长0.1 nm曝光— s × 16

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
GM-CSF/IL-2 inhibition factor
查看序列
MACLRVFLAVLALCGSVHSAQWIGERDFCTAHAQDVFARLQVWMRIDRNVTAADNSSACALAIETPPSNFDADVYVAAAGINVSVSAINCGFFNMRQVETTYNTARRQMYVYMDSWDPWVIDDPQPLFSQEYENETLPYLLEVLELARLYIRVGCTVPGEQPFEVIPGIDYPHTGMEFLQHVLRPNRRFAPAKLHMDLEVDHRCVSAVHVKAFLQDACSARKARTPLYFAGHGCNHPDRRPKNPVPRPQHVSSPISRKCSMQTAR
proteinOrf virusQ9J5U5—–—tetramer分子数 429.924 kDa
Granulocyte-macrophage colony-stimulating factor
查看序列
APTRQPSPVTRPWQHVDAIKEALSLLNDSTDTAAVMDETVEVVSEMFDSQEPTCLQTRLELYKQGLRGSLTSLTGSLTMMASHYKKHCPPTQETSCETQIITFKSFKENLKDFLFIIPFDCWEPVQK
proteinOvis ariesP2877318–144dimer分子数 214.411 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
11073[3]0.07607809–5.496227 1/nm含误差列缺失 02sasbdb/entries/89/sasda89/source/SASDA89.dat

2. SASBDB 报告的指标 Reported Results

指标方法数值误差单位
dmaxP(r)12.4nm
i0Guinier0.1513810.0001
i0P(r)0.1494
mwExperimental153.0kDa
mwGuinier I(0)153.0kDa
mwPorod144.0kDa
porod_volumePorod231.0nm³
rgGuinier3.790.13nm
rgP(r)3.77nm

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。

3. 来源拟合与模型 Source Fits & Models

4. 来源文件索引 Source Files

5. 实验说明与论文 Experiment & Publication

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缓冲液浓度20.0 mM
pH7.4添加剂150 mM NaCl
缓冲液说明
纯度测定方法SEC-SAXS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2014-09-10储存 / 测量温度— / 20.0
曝光时间帧数16
波长0.1样品-探测器距离1.82
光源X-ray synchrotron探测器AVIEX PCCD170170
机构 / 束线SOLEIL / SWING · Saint-Aubin, France
q 范围0.076 – 5.496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/89/sasda89/source/SASDA89.zipdownloaded315418b5486d6b7a77fd19fea0b97599ac83af24610fc6248fb2dd40c3f3177842fb5f下载查看原文件源站
pddfsasbdb/entries/89/sasda89/source/SASDA89.outdownloaded50065aadb9ace17565a22195d315ada011179a6d63ae9a5fccdf798c65a4aeaa8d9c8下载查看原文件源站
sascifsasbdb/entries/89/sasda89/source/SASDA89.sascifdownloaded14173818a7948c16edf6d39eb23163aed35b4b78be2b97dd2ebb11876df2feac30217f9下载查看原文件源站
summarysasbdb/entries/89/sasda89/source/summary.jsondownloaded8577ef98acffcb610f0e88efd11e97833834b0f2fbfb3d3636a3973ff0d01f04e6b2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:170 个字段值
字段路径原始值
codeSASDA89
statusPublished
type_of_curveOther
angular_unit1/nm
project.titleStructural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF.
project.publication.titleStructural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF.
project.publication.author_listFelix J, Kandiah E, De Munck S, Bloch Y, van Zundert GC, Pauwels K, Dansercoer A, Novanska K, Read RJ, Bonvin AM, Vergauwen B, Verstraete K, Gutsche I, Savvides SN
project.publication.journalNat Commun
project.publication.doi10.1038/ncomms13228
project.publication.pmid27819269
project.publication.published_date2016 Nov 7
project.statusreleased
project.submitted_date2015-08-07
project.released_date2016-12-16
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDA89.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDA89.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDA89_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDA89_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDA89_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDA89_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDA89.sascif
experiment.instrument.detector.typeCCD
experiment.instrument.detector.nameAVIEX PCCD170170
experiment.instrument.detector.resolutionnull
experiment.instrument.nameSOLEIL
experiment.instrument.citySaint-Aubin
experiment.instrument.countryFrance
experiment.instrument.beamline_nameSWING
experiment.instrument.beam_geometry
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_nameGM-CSF/IL-2 inhibition factor
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceMACLRVFLAVLALCGSVHSAQWIGERDFCTAHAQDVFARLQVWMRIDRNVTAADNSSACALAIETPPSNFDADVYVAAAGINVSVSAINCGFFNMRQVETTYNTARRQMYVYMDSWDPWVIDDPQPLFSQEYENETLPYLLEVLELARLYIRVGCTVPGEQPFEVIPGIDYPHTGMEFLQHVLRPNRRFAPAKLHMDLEVDHRCVSAVHVKAFLQDACSARKARTPLYFAGHGCNHPDRRPKNPVPRPQHVSSPISRKCSMQTAR
experiment.sample.molecule[0].organismOrf virus
experiment.sample.molecule[0].uniprot_codeQ9J5U5
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_sequenceMACLRVFLAVLALCGSVHSAQWIGERDFCTAHAQDVFARLQVWMRIDRNVTAADNSSACA LAIETPPSNFDADVYVAAAGINVSVSAINCGFFNMRQVETTYNTARRQMYVYMDSWDPWV IDDPQPLFSQEYENETLPYLLEVLELARLYIRVGCTVPGEQPFEVIPGIDYPHTGMEFLQ HVLRPNRRFAPAKLHMDLEVDHRCVSAVHVKAFLQDACSARKARTPLYFAGHGCNHPDRR PKNPVPRPQHVSSPISRKCSMQTAR
experiment.sample.molecule[0].mw29.924
experiment.sample.molecule[0].total_mw119.696
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.molecule[1].long_nameGranulocyte-macrophage colony-stimulating factor
experiment.sample.molecule[1].short_namenull
experiment.sample.molecule[1].sequenceAPTRQPSPVTRPWQHVDAIKEALSLLNDSTDTAAVMDETVEVVSEMFDSQEPTCLQTRLE LYKQGLRGSLTSLTGSLTMMASHYKKHCPPTQETSCETQIITFKSFKENLKDFLFIIPFD CWEPVQK
experiment.sample.molecule[1].organismOvis aries
experiment.sample.molecule[1].uniprot_codeP28773
experiment.sample.molecule[1].uniprot_range_first18
experiment.sample.molecule[1].uniprot_range_last144
experiment.sample.molecule[1].oligomerizationdimer
experiment.sample.molecule[1].molecular_typeprotein
experiment.sample.molecule[1].uniprot_sequenceMWLQNLLLLGTVVCSFSAPTRQPSPVTRPWQHVDAIKEALSLLNDSTDTAAVMDETVEVV SEMFDSQEPTCLQTRLELYKQGLRGSLTSLTGSLTMMASHYKKHCPPTQETSCETQIITF KSFKENLKDFLFIIPFDCWEPVQK
experiment.sample.molecule[1].mw14.411
experiment.sample.molecule[1].total_mw28.823
experiment.sample.molecule[1].number_molecules2
experiment.sample.molecule[1].complex_stateTrue
experiment.sample.molecule[1].deuterationnull
experiment.sample.molecule[1].molecule_sourcebiological
experiment.sample.molecule[1].molecule_descriptionnull
experiment.sample.buffer.name20 mM HEPES 150 mM NaCl
experiment.sample.buffer.concentration_unitmM
experiment.sample.buffer.commentnull
experiment.sample.buffer.additive150 mM NaCl
experiment.sample.buffer.concentration20.0
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.4
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodSEC-SAXS
experiment.sample.nameComplex between ovine GM-CSF and GM-CSF/IL-2 inhibition factor
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[]
experiment.contributor[0].contributor_nameJan
experiment.contributor[0].contributor_surnameFelix
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitmg/ml
experiment.date2014-09-10
experiment.storage_temperaturenull
experiment.cell_temperature20.0
experiment.exposure_timenull
experiment.number_of_frames16
experiment.wavelength0.1
experiment.sample_detector_distance1.82
experiment.concentration_minnull
experiment.concentration_max9.7
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.076
experiment.s_max5.496
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].softwareFoXS
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modelmix
fits[0].models[0].software_version
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fits[0].models[0].model_mw102.1
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].user29
fits[0].fit_unit1/A
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fits[0].softwarenull
fits[0].chi_square_value99.0
fits[0].p_value0.0
fits[0].fit_residual_plotSASDA89_fit1_fitresiduals_img.png
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fits[0].fit_lognull
fits[0].software_versionnull
fits[0].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionnull
i0_calibration_standardnull
descriptionModeling of SAXS data: The crystal structure of the GIF:oGM-CSF complex was used as an input for the Allosmod-FoXS web server to model missing loops, N- and C-termini and N-linked glycosylation. During each Allosmod-FoXS run, data up to a scattering angle of 0.5 Å-1 was used. Fits to the experimental SAXS data were calculated using the FoXS software.
experiment_descriptionX-ray synchrotron radiation scattering data from solutions of the complex between GM-CSF/IL-2 inhibition factor and ovine Granulocyte-macrophage colony-stimulating factor in 20 mM HEPES 150 mM NaCl were collected on the SWING camera on the storage ring SOLEIL (Saint-Aubin, France) using a CCD AVIEX detector (I(s) vs s, where s = 4π sin θ/λ, where 2θ is the scattering angle). One solute concentration of 10 mg/ml was measured. 10 successive 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 purity of the sample was obtained via SEC-SAXS.
tags[]
intensity_unitnull
experimental_mw153.0
experimental_mw_errornull
guinier_i0_mw153.0
guinier_i0_mw_errornull
porod_mw144.0
porod_mw_errornull
pddf_i00.1494
pddf_i0_errornull
guinier_i00.151381
guinier_i0_error0.0001
pddf_rg3.77
pddf_rg_errornull
guinier_rg3.79
guinier_rg_error0.13
pddf_dmax12.4
pddf_dmax_errornull
porod_volume231.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first17
guinier_point_last47
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDA89_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
codeSASDA89
statussuccess
started_at2026-08-11T16:08:07.778449+00:00
finished_at2026-08-11T16:08:23.035116+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": "SASDA89",
  "status": "Published",
  "type_of_curve": "Other",
  "angular_unit": "1/nm",
  "project": {
    "title": "Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF.",
    "publication": {
      "title": "Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF.",
      "author_list": "Felix J, Kandiah E, De Munck S, Bloch Y, van Zundert GC, Pauwels K, Dansercoer A, Novanska K, Read RJ, Bonvin AM, Vergauwen B, Verstraete K, Gutsche I, Savvides SN",
      "journal": "Nat Commun",
      "doi": "10.1038/ncomms13228",
      "pmid": "27819269",
      "published_date": "2016 Nov 7"
    },
    "status": "released",
    "submitted_date": "2015-08-07",
    "released_date": "2016-12-16"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDA89.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDA89.dat",
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  "experiment": {
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      "detector": {
        "type": "CCD",
        "name": "AVIEX PCCD170170",
        "resolution": null
      },
      "name": "SOLEIL",
      "city": "Saint-Aubin",
      "country": "France",
      "beamline_name": "SWING",
      "beam_geometry": "",
      "type_of_source": "X-ray synchrotron",
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      "line_collimation": null,
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          "organism": "Orf virus",
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          "oligomerization": "tetramer",
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          "oligomerization": "dimer",
          "molecular_type": "protein",
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      "buffer": {
        "name": "20 mM HEPES 150 mM NaCl",
        "concentration_unit": "mM",
        "comment": null,
        "additive": "150 mM NaCl",
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        "pka": null,
        "ph": 7.4,
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      "purity_method": "SEC-SAXS",
      "name": "Complex between ovine GM-CSF and GM-CSF/IL-2 inhibition factor",
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      "absorbption": null,
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    "contributor": [
      {
        "affiliation": [],
        "contributor_name": "Jan",
        "contributor_surname": "Felix",
        "orcid": null
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    "concentration_method": null,
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    "date": "2014-09-10",
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  "experiment_description": "X-ray synchrotron radiation scattering data from solutions of the complex between GM-CSF/IL-2 inhibition factor and ovine Granulocyte-macrophage colony-stimulating factor in 20 mM HEPES 150 mM NaCl were collected on the SWING camera on the storage ring SOLEIL (Saint-Aubin, France) using a CCD AVIEX detector (I(s) vs s, where s = 4π sin θ/λ, where 2θ is the scattering angle). One solute concentration of 10 mg/ml was measured. 10 successive 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 purity of the sample was obtained via SEC-SAXS.",
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  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
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}
查看完整 manifest.json 原文
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