SASDB76

Deglycosylated myelin-associated glycoprotein (immunoglobulin domains 1-3)

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

Endo-Hf-deglycosylated Myelin-associated glycoprotein (MAG) immunoglobulin domains 1-3

1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Deglycosylated myelin-associated glycoprotein (immunoglobulin domains 1-3)

浓度— – 1.39 缓冲液 / pH20 mM HEPES 150 mM NaCl / 7.5
Experimental temperature20.0 设备 / 束线ESRF / BM29
波长0.0992 nm曝光2.0 s × 10

分子组分

组分类型 / OrganismUniProt 与Construct寡聚状态Molecular weight
Myelin-associated glycoprotein Ig domains 1-3
查看序列
GSGHWGAWMPSTISAFEGTCVSIPCRFDFPDELRPAVVHGVWYFNSPYPKNYPPVVFKSRTQVVHESFQGRSRLLGDLGLRNCTLLLSTLSPELGGKYYFRGDLGGYNQYTFSEHSVLDIVNTPNIVVPPEVVAGTEVEVSCMVPDNCPELRPELSWLGHEGLGEPTVLGRLREDEGTWVQVSLLHFVPTREANGHRLGCQAAFPNTTLQFEGYASLDVKYPPVIVEMNSSVEAIEGSHVSLLCGADSNPPPLLTWMRDGMVLREAVAKSLYLDLEEVTPGEDGVYACLAENAYGQDNRTVELSVMYAAAAHHHHHH
proteinMus musculusP2091720–325monomer分子数 134.98 kDa

实验曲线

曲线点数 / 列q range误差质量负强度点来源文件
11043[3]0.0363402–4.969332 1/nm含误差列缺失 044sasbdb/entries/76/sasdb76/source/SASDB76.dat

2. SASBDB 报告的指标 Reported Results

指标方法数值误差单位
dmaxP(r)12.6nm
i0Guinier39.9
i0P(r)39.3
mwExperimental36.6kDa
mwGuinier I(0)39.9kDa
mwPorod28.8kDa
porod_volumePorod49.4nm³
rgGuinier3.9nm
rgP(r)3.9nm

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

拟合 1 · —

χ²:3.85CorMap p:0.0单位:1/A
模型名称 / 类型软件Symmetry模型 MWPDB 声明来源文件
1atomicPDB (Protein Data Bank) 2.8.334.095LFR模型 图片

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“—”;Not declared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
pH7.5添加剂150 mM NaCl
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2014-09-11储存 / 测量温度20.0 / 20.0
曝光时间2.0帧数10
波长0.0992样品-探测器距离2.87
光源X-ray synchrotron探测器Pilatus 1M
机构 / 束线ESRF / BM29 · Grenoble, France
q range0.036 – 4.969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Download文件

类别文件状态大小校验值Download与查看
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summarysasbdb/entries/76/sasdb76/source/summary.jsondownloaded81773f5667d4dde72fc6b29172ff738bf649c14c005cca46ec9d42ac0396e64cfd5bDownload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
codeSASDB76
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleStructural basis of myelin-associated glycoprotein adhesion and signalling.
project.publication.titleStructural basis of myelin-associated glycoprotein adhesion and signalling.
project.publication.author_listPronker MF, Lemstra S, Snijder J, Heck AJ, Thies-Weesie DM, Pasterkamp RJ, Janssen BJ
project.publication.journalNat Commun
project.publication.doi10.1038/ncomms13584
project.publication.pmid27922006
project.publication.published_date2016 Dec 6
project.statusreleased
project.submitted_date2016-07-24
project.released_date2016-12-13
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experiment.instrument.detector.typeDectris
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
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_nameMyelin-associated glycoprotein Ig domains 1-3
experiment.sample.molecule[0].short_nameMAG
experiment.sample.molecule[0].sequenceGSGHWGAWMPSTISAFEGTCVSIPCRFDFPDELRPAVVHGVWY FNSPYPKNYPPVVFKSRTQVVHESFQGRSRLLGDLGLRNCTLLLSTLSPELGGKYYFRGD LGGYNQYTFSEHSVLDIVNTPNIVVPPEVVAGTEVEVSCMVPDNCPELRPELSWLGHEGL GEPTVLGRLREDEGTWVQVSLLHFVPTREANGHRLGCQAAFPNTTLQFEGYASLDVKYPP VIVEMNSSVEAIEGSHVSLLCGADSNPPPLLTWMRDGMVLREAVAKSLYLDLEEVTPGED GVYACLAENAYGQDNRTVELSVMYAAAAHHHHHH
experiment.sample.molecule[0].organismMus musculus
experiment.sample.molecule[0].uniprot_codeP20917
experiment.sample.molecule[0].uniprot_range_first20
experiment.sample.molecule[0].uniprot_range_last325
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
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experiment.sample.molecule[0].mw34.98
experiment.sample.molecule[0].total_mw34.98
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.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.ph7.5
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameDeglycosylated myelin-associated glycoprotein (immunoglobulin domains 1-3)
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].addressUtrecht, Netherlands
experiment.contributor[0].affiliation[0].full_nameUtrecht University
experiment.contributor[0].affiliation[0].webpagehttp://www.uu.nl/
experiment.contributor[0].contributor_nameMatti
experiment.contributor[0].contributor_surnamePronker
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2014-09-11
experiment.storage_temperature20.0
experiment.cell_temperature20.0
experiment.exposure_time2.0
experiment.number_of_frames10
experiment.wavelength0.0992
experiment.sample_detector_distance2.87
experiment.concentration_minnull
experiment.concentration_max1.39
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.036
experiment.s_max4.969
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_code5lfr
fits[0].models[0].pdb_link[0].ext_code5LFR
fits[0].models[0].pdb_link[0].ext_typepdb
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fits[0].models[0].bead_radius1.9
fits[0].models[0].lognull
fits[0].models[0].symmetry
fits[0].models[0].commentGlycans were trimmed off the model to match the SAXS curve of the deglycosylated sample
fits[0].models[0].user52
fits[0].fit_unit1/A
fits[0].fit_plothttps://www.sasbdb.org/media/fitting_files/scattering_plots/SASDB76_fit1_fit_img.png
fits[0].softwarenull
fits[0].chi_square_value3.85
fits[0].p_value0.0
fits[0].fit_residual_plotnull
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fits[0].fit_lognull
fits[0].software_versionnull
fits[0].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionGnom 4.6
i0_calibration_standardnull
descriptionEndo-Hf-deglycosylated Myelin-associated glycoprotein (MAG) immunoglobulin domains 1-3
experiment_descriptionSynchrotron SAXS data from solutions of deglycosylated myelin-associated glycoprotein (Ig domains 1-3) in HEPES, pH 7.5 were collected on the BM29 camera on the storage ring ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4π sin θ/λ and 2θ is the scattering angle). One solute concentration of 1.39 mg/ml was measured at 20°C. 10 successive 2 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 curve was scaled to protein concentration.
tags[]
intensity_unitnull
experimental_mw36.6
experimental_mw_errornull
guinier_i0_mw39.9
guinier_i0_mw_errornull
porod_mw28.8
porod_mw_errornull
pddf_i039.3
pddf_i0_errornull
guinier_i039.9
guinier_i0_errornull
pddf_rg3.9
pddf_rg_errornull
guinier_rg3.9
guinier_rg_errornull
pddf_dmax12.6
pddf_dmax_errornull
porod_volume49.4
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first25
guinier_point_last52
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDB76_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
codeSASDB76
statussuccess
started_at2026-08-11T16:47:45.039867+00:00
finished_at2026-08-11T16:47:54.197606+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": "SASDB76",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Structural basis of myelin-associated glycoprotein adhesion and signalling.",
    "publication": {
      "title": "Structural basis of myelin-associated glycoprotein adhesion and signalling.",
      "author_list": "Pronker MF, Lemstra S, Snijder J, Heck AJ, Thies-Weesie DM, Pasterkamp RJ, Janssen BJ",
      "journal": "Nat Commun",
      "doi": "10.1038/ncomms13584",
      "pmid": "27922006",
      "published_date": "2016 Dec 6"
    },
    "status": "released",
    "submitted_date": "2016-07-24",
    "released_date": "2016-12-13"
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    "sample": {
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          "uniprot_sequence": "MIFLATLPLFWIMISASRGGHWGAWMPSTISAFEGTCVSIPCRFDFPDELRPAVVHGVWY\nFNSPYPKNYPPVVFKSRTQVVHESFQGRSRLLGDLGLRNCTLLLSTLSPELGGKYYFRGD\nLGGYNQYTFSEHSVLDIVNTPNIVVPPEVVAGTEVEVSCMVPDNCPELRPELSWLGHEGL\nGEPTVLGRLREDEGTWVQVSLLHFVPTREANGHRLGCQAAFPNTTLQFEGYASLDVKYPP\nVIVEMNSSVEAIEGSHVSLLCGADSNPPPLLTWMRDGMVLREAVAKSLYLDLEEVTPGED\nGVYACLAENAYGQDNRTVELSVMYAPWKPTVNGTVVAVEGETVSILCSTQSNPDPILTIF\nKEKQILATVIYESQLQLELPAVTPEDDGEYWCVAENQYGQRATAFNLSVEFAPIILLESH\nCAAARDTVQCLCVVKSNPEPSVAFELPSRNVTVNETEREFVYSERSGLLLTSILTIRGQA\nQAPPRVICTSRNLYGTQSLELPFQGAHRLMWAKIGPVGAVVAFAILIAIVCYITQTRRKK\nNVTESSSFSGGDNPHVLYSPEFRISGAPDKYESEKQRLGSERRLLGLRGESPELDLSYSH\nSDLGKRPTKDSYTLTEELAEYAEIRVK",
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          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
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        "concentration_unit": "mM",
        "comment": null,
        "additive": "150 mM NaCl",
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        "pka": null,
        "ph": 7.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Deglycosylated myelin-associated glycoprotein (immunoglobulin domains 1-3)",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
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      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Utrecht, Netherlands",
            "full_name": "Utrecht University",
            "webpage": "http://www.uu.nl/"
          }
        ],
        "contributor_name": "Matti",
        "contributor_surname": "Pronker",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2014-09-11",
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    "cell_temperature": 20.0,
    "exposure_time": 2.0,
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        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDB76_fit1_model1_img.png",
          "software": "PDB (Protein Data Bank)",
          "pdb_link": [
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              "ext_code": "5LFR",
              "ext_type": "pdb",
              "difference_with_model": "derived"
            }
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          "log": null,
          "symmetry": "",
          "comment": "Glycans were trimmed off the model to match the SAXS curve of the deglycosylated sample",
          "user": 52
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      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDB76_fit1_fit_img.png",
      "software": null,
      "chi_square_value": 3.85,
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  "description": "Endo-Hf-deglycosylated Myelin-associated glycoprotein (MAG) immunoglobulin domains 1-3",
  "experiment_description": "Synchrotron SAXS data from solutions of deglycosylated myelin-associated glycoprotein (Ig domains 1-3) in HEPES, pH 7.5 were collected on the BM29 camera on the storage ring ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4π sin θ/λ and 2θ is the scattering angle). One solute concentration of 1.39 mg/ml was measured at 20°C. 10 successive 2 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 curve was scaled to protein concentration.",
  "tags": [],
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  "intensities_log_log_plot": "SASDB76_datloglog_img.png",
  "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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