SASDER5

AICAR/fumarate-bound neanderthal adenylosuccinate lyase (ADSL)

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Single concentration 最后更新:2022-03-31T21:47:30.462058+02:00
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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · AICAR/fumarate-bound neanderthal adenylosuccinate lyase (ADSL)

浓度— – 5.0 缓冲液 / pH10 mM HEPES, 100 mM NaCl, 1 mM DTT, 1 mM 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR), 1mM Fumarate / 7.5
实验温度20.0 设备 / 束线ESRF / BM29
波长0.099 nm曝光1.0 s × 10

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
Adenylosuccinate lyase
查看序列
GSHMAAGGDHGSPDSYRSPLASRYASPEMCFVFSDRYKFRTWRQLWLWLAEAEQTLGLPITDEQIQEMKSNLENIDFKMAAEEEKRLRHDVMAHVHTFGHCCPKAAGIIHLGATSCYVGDNTDLIILRNALDLLLPKLARVISRLADFAKERASLPTLGFTHFQPAQLTTVGKRCCLWIQDLCMDLQNLKRVRDDLRFRGVKGTTGTQASFLQLFEGDDHKVEQLDKMVTEKAGFKRAFIITGQTYTRKVDIEVLSVLASLGASVHKICTDIRLLANLKEMEEPFEKQQIGSSAMPYKRNPMRSERCCSLARHLMTLVMDPLQTASVQWFERTLDDSANRRICLAEAFLTADTILNTLQNISEGLVVYPKVIERRIRQELPFMATENIIMAMVKAGGSRQDCHEKIRVLSQQAASVVKQEGGDNDLIERIQADAYFSPIHSQLDHLLDPSSFTGRASQQVQRFLEEEVYPLLKPYESVMKVKAELCL
proteinHomo sapiens neanderthalensisA0A384E0N41–487tetramer分子数 455.142 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
1796[3]0.04673647–3.803532 1/nm含误差列缺失 00sasbdb/entries/r5/sasder5/source/SASDER5.dat
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2. SASBDB 报告的指标 Reported Results

指标方法数值误差单位
i0Guinier152.020.07arbitrary
mwExperimental161.0—kDa
mwPorod158.0—kDa
porod_volumePorod252.0—nm³
rgGuinier3.620.01nm

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

拟合 1 · CRYSOL

χ²:11.538CorMap p:0.0单位:1/A
模型名称 / 类型软件对称性模型 MWPDB 声明来源文件
1—atomicPDB (Protein Data Bank) —213.05NXA模型 图片
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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10 mM HEPES, 100 mM NaCl, 1 mM DTT, 1 mM 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR), 1mM Fumarate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2016-07-24储存 / 测量温度20.0 / 20.0
曝光时间1.0帧数10
波长0.099样品-探测器距离2.864
光源X-ray synchrotron探测器Pilatus 1M
机构 / 束线ESRF / BM29 · Grenoble, France
q 范围0.047 – 3.804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

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/r5/sasder5/source/SASDER5.zipdownloaded3281419d5e72b3843397fa318796eb7c6d3833e7a7bb02a97ef9f7c940583743567664下载查看原文件源站
pddfsasbdb/entries/r5/sasder5/source/SASDER5.outnot_listed——下载查看原文件
sascifsasbdb/entries/r5/sasder5/source/SASDER5.sascifdownloaded1651807a862d360d22fa79c931b679ffa16b7a475a49b48518422442e70221dc76ae222下载查看原文件源站
summarysasbdb/entries/r5/sasder5/source/summary.jsondownloaded80804b40956259901f97f4749f513a65a10377468ccf03226c593435e65b35837105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(3 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
codeSASDER5
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleMolecular comparison of Neanderthal and Modern Human adenylosuccinate lyase.
project.publication.titleMolecular comparison of Neanderthal and Modern Human adenylosuccinate lyase.
project.publication.author_listVan Laer B, Kapp U, Soler-Lopez M, Moczulska K, Pääbo S, Leonard G, Mueller-Dieckmann C
project.publication.journalSci Rep
project.publication.doi10.1038/s41598-018-36195-5
project.publication.pmid30573755
project.publication.published_date2018 Dec 20
project.statusreleased
project.submitted_date2018-10-03
project.released_date2019-01-16
pddf_datanull
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDER5.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDER5_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDER5_kratky_img.png
pddf_plotnull
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDER5_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDER5.sascif
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_nameAdenylosuccinate lyase
experiment.sample.molecule[0].short_nameADSL
experiment.sample.molecule[0].sequenceGSHMAAGGDHGSPDSYRSPLASRYASPEMCFVFSDRYKFRTWR QLWLWLAEAEQTLGLPITDEQIQEMKSNLENIDFKMAAEEEKRLRHDVMAHVHTFGHCCP KAAGIIHLGATSCYVGDNTDLIILRNALDLLLPKLARVISRLADFAKERASLPTLGFTHF QPAQLTTVGKRCCLWIQDLCMDLQNLKRVRDDLRFRGVKGTTGTQASFLQLFEGDDHKVE QLDKMVTEKAGFKRAFIITGQTYTRKVDIEVLSVLASLGASVHKICTDIRLLANLKEMEE PFEKQQIGSSAMPYKRNPMRSERCCSLARHLMTLVMDPLQTASVQWFERTLDDSANRRIC LAEAFLTADTILNTLQNISEGLVVYPKVIERRIRQELPFMATENIIMAMVKAGGSRQDCH EKIRVLSQQAASVVKQEGGDNDLIERIQADAYFSPIHSQLDHLLDPSSFTGRASQQVQRF LEEEVYPLLKPYESVMKVKAELCL
experiment.sample.molecule[0].organismHomo sapiens neanderthalensis
experiment.sample.molecule[0].uniprot_codeA0A384E0N4
experiment.sample.molecule[0].uniprot_range_first1
experiment.sample.molecule[0].uniprot_range_last487
experiment.sample.molecule[0].oligomerizationtetramer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceGSHMAAGGDHGSPDSYRSPLASRYASPEMCFVFSDRYKFRTWRQLWLWLAEAEQTLGLPI TDEQIQEMKSNLENIDFKMAAEEEKRLRHDVMAHVHTFGHCCPKAAGIIHLGATSCYVGD NTDLIILRNALDLLLPKLARVISRLADFAKERASLPTLGFTHFQPAQLTTVGKRCCLWIQ DLCMDLQNLKRVRDDLRFRGVKGTTGTQASFLQLFEGDDHKVEQLDKMVTEKAGFKRAFI ITGQTYTRKVDIEVLSVLASLGASVHKICTDIRLLANLKEMEEPFEKQQIGSSAMPYKRN PMRSERCCSLARHLMTLVMDPLQTASVQWFERTLDDSANRRICLAEAFLTADTILNTLQN ISEGLVVYPKVIERRIRQELPFMATENIIMAMVKAGGSRQDCHEKIRVLSQQAASVVKQE GGDNDLIERIQADAYFSPIHSQLDHLLDPSSFTGRASQQVQRFLEEEVYPLLKPYESVMK VKAELCL
experiment.sample.molecule[0].mw55.142
experiment.sample.molecule[0].total_mw220.568
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_description
experiment.sample.buffer.name10 mM HEPES, 100 mM NaCl, 1 mM DTT, 1 mM 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR), 1mM Fumarate
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.nameAICAR/fumarate-bound neanderthal adenylosuccinate lyase (ADSL)
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_nameESRF
experiment.contributor[0].affiliation[0].addressGrenoble, France
experiment.contributor[0].affiliation[0].full_nameEuropean Synchrotron Radiation Facility
experiment.contributor[0].affiliation[0].webpagehttp://www.esrf.eu/
experiment.contributor[0].contributor_nameBart
experiment.contributor[0].contributor_surnameVan Laer
experiment.contributor[0].orcid
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2016-07-24
experiment.storage_temperature20.0
experiment.cell_temperature20.0
experiment.exposure_time1.0
experiment.number_of_frames10
experiment.wavelength0.099
experiment.sample_detector_distance2.864
experiment.concentration_minnull
experiment.concentration_max5.0
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.047
experiment.s_max3.804
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDER5_fit1_model1_img.png
fits[0].models[0].softwarePDB (Protein Data Bank)
fits[0].models[0].pdb_link[0].pdb_code5nxa
fits[0].models[0].pdb_link[0].ext_code5NXA
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_versionnull
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fits[0].models[0].model_mw213.0
fits[0].models[0].bead_radiusnull
fits[0].models[0].lognull
fits[0].models[0].symmetrynull
fits[0].models[0].commentnull
fits[0].models[0].user371
fits[0].fit_unit1/A
fits[0].fit_plothttps://www.sasbdb.org/media/fitting_files/scattering_plots/SASDER5_fit1_fixed_fit_img.png
fits[0].softwareCRYSOL
fits[0].chi_square_value11.538
fits[0].p_value0.0
fits[0].fit_residual_plotnull
fits[0].fit_datahttps://www.sasbdb.org/media/fitting_files/SASDER5_fit1.fit
fits[0].fit_lognull
fits[0].software_versionnull
fits[0].description
estimated_volume_methodnull
pddf_softwarenull
pddf_software_versionnull
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of AICAR/fumarate-bound neanderthal adenylosuccinate lyase (ADSL) in 10 mM HEPES, 100 mM NaCl, 1 mM DTT, 1 mM 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR), 1 mM Fumarate, pH 7.5 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Dectris Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.099 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 5.00 mg/ml was measured at 20°C. 10 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_mw161.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw158.0
porod_mw_errornull
pddf_i0null
pddf_i0_errornull
guinier_i0152.02
guinier_i0_error0.07
pddf_rgnull
pddf_rg_errornull
guinier_rg3.62
guinier_rg_error0.01
pddf_dmaxnull
pddf_dmax_errornull
porod_volume252.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first20
guinier_point_last67
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDER5_datloglog_img.png
symmetrynull
last_modified2022-03-31T21:47:30.462058+02:00
bragg_peak[]
manifest.json:33 个字段值
字段路径原始值
codeSASDER5
statussuccess
started_at2026-08-11T14:53:52.203534+00:00
finished_at2026-08-11T14:54:05.626201+00:00
source_last_modified2022-03-31T21:47:30.462058+02:00
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查看完整 summary.json 原文
{
  "code": "SASDER5",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Molecular comparison of Neanderthal and Modern Human adenylosuccinate lyase.",
    "publication": {
      "title": "Molecular comparison of Neanderthal and Modern Human adenylosuccinate lyase.",
      "author_list": "Van Laer B, Kapp U, Soler-Lopez M, Moczulska K, Pääbo S, Leonard G, Mueller-Dieckmann C",
      "journal": "Sci Rep",
      "doi": "10.1038/s41598-018-36195-5",
      "pmid": "30573755",
      "published_date": "2018 Dec 20"
    },
    "status": "released",
    "submitted_date": "2018-10-03",
    "released_date": "2019-01-16"
  },
  "pddf_data": null,
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  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDER5.sascif",
  "experiment": {
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      },
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      "city": "Grenoble",
      "country": "France",
      "beamline_name": "BM29",
      "beam_geometry": "",
      "type_of_source": "X-ray synchrotron",
      "point_source": null,
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    },
    "sample": {
      "molecule": [
        {
          "long_name": "Adenylosuccinate lyase",
          "short_name": "ADSL",
          "sequence": "GSHMAAGGDHGSPDSYRSPLASRYASPEMCFVFSDRYKFRTWR\r\nQLWLWLAEAEQTLGLPITDEQIQEMKSNLENIDFKMAAEEEKRLRHDVMAHVHTFGHCCP\r\nKAAGIIHLGATSCYVGDNTDLIILRNALDLLLPKLARVISRLADFAKERASLPTLGFTHF\r\nQPAQLTTVGKRCCLWIQDLCMDLQNLKRVRDDLRFRGVKGTTGTQASFLQLFEGDDHKVE\r\nQLDKMVTEKAGFKRAFIITGQTYTRKVDIEVLSVLASLGASVHKICTDIRLLANLKEMEE\r\nPFEKQQIGSSAMPYKRNPMRSERCCSLARHLMTLVMDPLQTASVQWFERTLDDSANRRIC\r\nLAEAFLTADTILNTLQNISEGLVVYPKVIERRIRQELPFMATENIIMAMVKAGGSRQDCH\r\nEKIRVLSQQAASVVKQEGGDNDLIERIQADAYFSPIHSQLDHLLDPSSFTGRASQQVQRF\r\nLEEEVYPLLKPYESVMKVKAELCL",
          "organism": "Homo sapiens neanderthalensis",
          "uniprot_code": "A0A384E0N4",
          "uniprot_range_first": 1,
          "uniprot_range_last": 487,
          "oligomerization": "tetramer",
          "molecular_type": "protein",
          "uniprot_sequence": "GSHMAAGGDHGSPDSYRSPLASRYASPEMCFVFSDRYKFRTWRQLWLWLAEAEQTLGLPI\nTDEQIQEMKSNLENIDFKMAAEEEKRLRHDVMAHVHTFGHCCPKAAGIIHLGATSCYVGD\nNTDLIILRNALDLLLPKLARVISRLADFAKERASLPTLGFTHFQPAQLTTVGKRCCLWIQ\nDLCMDLQNLKRVRDDLRFRGVKGTTGTQASFLQLFEGDDHKVEQLDKMVTEKAGFKRAFI\nITGQTYTRKVDIEVLSVLASLGASVHKICTDIRLLANLKEMEEPFEKQQIGSSAMPYKRN\nPMRSERCCSLARHLMTLVMDPLQTASVQWFERTLDDSANRRICLAEAFLTADTILNTLQN\nISEGLVVYPKVIERRIRQELPFMATENIIMAMVKAGGSRQDCHEKIRVLSQQAASVVKQE\nGGDNDLIERIQADAYFSPIHSQLDHLLDPSSFTGRASQQVQRFLEEEVYPLLKPYESVMK\nVKAELCL",
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          "molecule_source": "biological",
          "molecule_description": ""
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      "buffer": {
        "name": "10 mM HEPES, 100 mM NaCl, 1 mM DTT, 1 mM 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR), 1mM Fumarate",
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      },
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      "name": "AICAR/fumarate-bound neanderthal adenylosuccinate lyase (ADSL)",
      "ext_coefficient": null,
      "contrast": null,
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      "dry_vol": null,
      "absorbption": null,
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    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": "ESRF",
            "address": "Grenoble, France",
            "full_name": "European Synchrotron Radiation Facility",
            "webpage": "http://www.esrf.eu/"
          }
        ],
        "contributor_name": "Bart",
        "contributor_surname": "Van Laer",
        "orcid": ""
      }
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    "concentration_unit": null,
    "date": "2016-07-24",
    "storage_temperature": 20.0,
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          "software": "PDB (Protein Data Bank)",
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              "difference_with_model": "derived"
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      "fit_unit": "1/A",
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  "experiment_description": "Synchrotron SAXS data from solutions of AICAR/fumarate-bound neanderthal adenylosuccinate lyase (ADSL) in 10 mM HEPES, 100 mM NaCl, 1 mM DTT, 1 mM 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR), 1 mM Fumarate, pH 7.5 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Dectris Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.099 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 5.00 mg/ml was measured at 20°C. 10 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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  "symmetry": null,
  "last_modified": "2022-03-31T21:47:30.462058+02:00",
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}
查看完整 manifest.json 原文
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