SASDA76

NetrinVIV DCC56 complex

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Single concentration 最后更新:2023-06-21T07:56:39.492710+02:00

1. 样品、组分与实验条件 Sample & Experiment

样品 1 · NetrinVIV DCC56 complex

浓度0.3 – 2.9 缓冲液 / pH25 MES mM 200 mM NaCl 50 mM Tris 0.2 M ammonium sulfate (NH4)2(SO4) 1mM calcium chloride CaCl2 / 7.0
实验温度10.0 设备 / 束线PETRA III / EMBL P12
波长0.12 nm曝光0.05 s × 20

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
Netrin-1
查看序列
GPGLSMFAGQAAQPDPCSDENGHPRRCIPDFVNAAFGKDVRVSSTCGRPPARYCVVSERGEERLRSCHLCNASDPKKAHPPAFLTDLNNPHNLTCWQSENYLQFPHNVTLTLSLGKKFEVTYVSLQFCSPRPESMAIYKSMDYGRTWVPFQFYSTQCRKMYNRPHRAPITKQNEQEAVCTDSHTDMRPLSGGLIAFSTLDGRPSAHDFDNSPVLQDWVTATDIRVAFSRLHTFGDENEDDSELARDSYFYAVSDLQVGGRCKCNGHAARCVRDRDDSLVCDCRHNTAGPECDRCKPFHYDRPWQRATAREANECVACNCNLHARRCRFNMELYKLSGRKSGGVCLNCRHNTAGRHCHYCKEGYYRDMGKPITHRKACKACDCHPVGAAGKTCNQTTGQCPCKDGVTGITCNRCAKGYQQSRSPIAPCIKELHHHHHH
proteinHomo sapiensO95631—–—monomer分子数 149.1 kDa
Deleted in Colorectal Cancer (FN5 & FN6)
查看序列
MLPPVGVQAVALTHDAVRVSWADNSVPKNQKTSEVRLYTVRWRTSFSASAKYKSEDTTSLSYTATGLKPNTMYEFSVMVTKNRRSSTWSMTAHATTYEAAPTSAPKDLTVITREGKPRAVIVSWQPPLEANGKITAYILFYTLDKNIPIDDWIMETISGDRLTHQIMDLNLDTMYYFRIQARNSKGVGPLSDPILFRTLKLEVLFQGPGGHHHHHHGGWSHPQFEK
proteinHomo sapiens—–—monomer分子数 125.5 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
11723[3]0.0535586–3.49486 1/nm含误差列缺失 0174sasbdb/entries/76/sasda76/source/SASDA76.dat

2. SASBDB 报告的指标 Reported Results

指标方法数值误差单位
dmaxP(r)17.0nm
i0Guinier1370.0
i0P(r)1450.0
mwExperimental49.0kDa
porod_volumePorod120.0nm³
rgGuinier5.1nm
rgP(r)5.1nm

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

该条目没有来源拟合记录。

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25 MES mM 200 mM NaCl 50 mM Tris 0.2 M ammonium sulfate (NH4)2(SO4) 1mM calcium chloride CaCl2缓冲液浓度25.0 mM
pH7.0添加剂NaCl 200.000 mM, Tris 50.000 mM, (NH4)2(SO4) 0.200 M ammonium sulfate, CaCl2 1.000 mM calcium chloride
缓冲液说明MES/TRIS
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2013-10-31储存 / 测量温度10.0 / 10.0
曝光时间0.05帧数20
波长0.12样品-探测器距离3.1
光源X-ray synchrotron探测器Pilatus 2M
机构 / 束线PETRA III / EMBL P12 · DESY; Hamburg, Germany
q 范围0.054 – 3.495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
curvesasbdb/entries/76/sasda76/source/SASDA76.datdownloaded77848553bd27292fc325e88e4df4939ee01193cc3e770a9822be35e3ede9b0cfec557下载查看原文件源站
full_entry_zipsasbdb/entries/76/sasda76/source/SASDA76.zipdownloaded31350cb89e4df68bc3068c36a90ebea4df28a73b100b2e075547f51efebcd3fd41807下载查看原文件源站
pddfsasbdb/entries/76/sasda76/source/SASDA76.outdownloaded33388d620813c72da09bce73dd712efd9711fa26a691137df8280f9c984edb4fc0825下载查看原文件源站
sascifsasbdb/entries/76/sasda76/source/SASDA76.sascifdownloaded120980c58d22c366b2117ddb7ddd55c874ff9d30d3750c2dc2794a87614a6730c5e96b下载查看原文件源站
summarysasbdb/entries/76/sasda76/source/summary.jsondownloaded74143b49b1e8cf9387d2c3eda81606452f94b21f98185ac358fae7560cacdd36b1a4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(2 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:151 个字段值
字段路径原始值
codeSASDA76
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleThe crystal structure of netrin-1 in complex with DCC reveals the bifunctionality of netrin-1 as a guidance cue.
project.publication.titleThe crystal structure of netrin-1 in complex with DCC reveals the bifunctionality of netrin-1 as a guidance cue.
project.publication.author_listFinci LI, Krüger N, Sun X, Zhang J, Chegkazi M, Wu Y, Schenk G, Mertens HDT, Svergun DI, Zhang Y, Wang JH, Meijers R
project.publication.journalNeuron
project.publication.doi10.1016/j.neuron.2014.07.010
project.publication.pmid25123307
project.publication.published_date2014 Aug 20
project.statusreleased
project.submitted_datenull
project.released_date2015-07-07
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDA76.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDA76.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDA76_dat_img.png
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pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDA76_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDA76_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDA76.sascif
experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus 2M
experiment.instrument.detector.resolutionnull
experiment.instrument.namePETRA III
experiment.instrument.cityDESY; Hamburg
experiment.instrument.countryGermany
experiment.instrument.beamline_nameEMBL P12
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_nameNetrin-1
experiment.sample.molecule[0].short_nameNetrinVIV
experiment.sample.molecule[0].sequenceGPGLSMFAGQAAQPDPCSDENGHPRRCIPDFVNAAFGKDVRVSSTCGRPPARYCVVSERGEERLRSCHLCNASDPKKAHPPAFLTDLNNPHNLTCWQSENYLQFPHNVTLTLSLGKKFEVTYVSLQFCSPRPESMAIYKSMDYGRTWVPFQFYSTQCRKMYNRPHRAPITKQNEQEAVCTDSHTDMRPLSGGLIAFSTLDGRPSAHDFDNSPVLQDWVTATDIRVAFSRLHTFGDENEDDSELARDSYFYAVSDLQVGGRCKCNGHAARCVRDRDDSLVCDCRHNTAGPECDRCKPFHYDRPWQRATAREANECVACNCNLHARRCRFNMELYKLSGRKSGGVCLNCRHNTAGRHCHYCKEGYYRDMGKPITHRKACKACDCHPVGAAGKTCNQTTGQCPCKDGVTGITCNRCAKGYQQSRSPIAPCIKELHHHHHH
experiment.sample.molecule[0].organismHomo sapiens
experiment.sample.molecule[0].uniprot_codeO95631
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMMRAVWEALAALAAVACLVGAVRGGPGLSMFAGQAAQPDPCSDENGHPRRCIPDFVNAAF GKDVRVSSTCGRPPARYCVVSERGEERLRSCHLCNASDPKKAHPPAFLTDLNNPHNLTCW QSENYLQFPHNVTLTLSLGKKFEVTYVSLQFCSPRPESMAIYKSMDYGRTWVPFQFYSTQ CRKMYNRPHRAPITKQNEQEAVCTDSHTDMRPLSGGLIAFSTLDGRPSAHDFDNSPVLQD WVTATDIRVAFSRLHTFGDENEDDSELARDSYFYAVSDLQVGGRCKCNGHAARCVRDRDD SLVCDCRHNTAGPECDRCKPFHYDRPWQRATAREANECVACNCNLHARRCRFNMELYKLS GRKSGGVCLNCRHNTAGRHCHYCKEGYYRDMGKPITHRKACKACDCHPVGAAGKTCNQTT GQCPCKDGVTGITCNRCAKGYQQSRSPIAPCIKIPVAPPTTAASSVEEPEDCDSYCKASK GKLKINMKKYCKKDYAVQIHILKADKAGDWWKFTVNIISVYKQGTSRIRRGDQSLWIRSR DIACKCPKIKPLKKYLLLGNAEDSPDQSGIVADKSSLVIQWRDTWARRLRKFQQREKKGK CKKA
experiment.sample.molecule[0].mw49.1
experiment.sample.molecule[0].total_mw49.1
experiment.sample.molecule[0].number_molecules1
experiment.sample.molecule[0].complex_statenull
experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
experiment.sample.molecule[0].molecule_descriptionnull
experiment.sample.molecule[1].long_nameDeleted in Colorectal Cancer (FN5 & FN6)
experiment.sample.molecule[1].short_namedcc56
experiment.sample.molecule[1].sequenceMLPPVGVQAVALTHDAVRVSWADNSVPKNQKTSEVRLYTVRWRTSFSASAKYKSEDTTSLSYTATGLKPNTMYEFSVMVTKNRRSSTWSMTAHATTYEAAPTSAPKDLTVITREGKPRAVIVSWQPPLEANGKITAYILFYTLDKNIPIDDWIMETISGDRLTHQIMDLNLDTMYYFRIQARNSKGVGPLSDPILFRTLKLEVLFQGPGGHHHHHHGGWSHPQFEK
experiment.sample.molecule[1].organismHomo sapiens
experiment.sample.molecule[1].uniprot_codenull
experiment.sample.molecule[1].uniprot_range_firstnull
experiment.sample.molecule[1].uniprot_range_lastnull
experiment.sample.molecule[1].oligomerizationmonomer
experiment.sample.molecule[1].molecular_typeprotein
experiment.sample.molecule[1].uniprot_sequencenull
experiment.sample.molecule[1].mw25.5
experiment.sample.molecule[1].total_mw25.5
experiment.sample.molecule[1].number_molecules1
experiment.sample.molecule[1].complex_statenull
experiment.sample.molecule[1].deuterationnull
experiment.sample.molecule[1].molecule_sourcebiological
experiment.sample.molecule[1].molecule_descriptionnull
experiment.sample.buffer.name25 MES mM 200 mM NaCl 50 mM Tris 0.2 M ammonium sulfate (NH4)2(SO4) 1mM calcium chloride CaCl2
experiment.sample.buffer.concentration_unitmM
experiment.sample.buffer.commentMES/TRIS
experiment.sample.buffer.additiveNaCl 200.000 mM, Tris 50.000 mM, (NH4)2(SO4) 0.200 M ammonium sulfate, CaCl2 1.000 mM calcium chloride
experiment.sample.buffer.concentration25.0
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.0
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameNetrinVIV DCC56 complex
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_nameEMBL-Hamburg
experiment.contributor[0].affiliation[0].addressNotkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany
experiment.contributor[0].affiliation[0].full_nameEuropean Molecular Biology Laboratory (EMBL) - Hamburg outstation
experiment.contributor[0].affiliation[0].webpagehttp://www.embl-hamburg.de/index.php
experiment.contributor[0].contributor_nameHaydyn
experiment.contributor[0].contributor_surnameMertens
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2013-10-31
experiment.storage_temperature10.0
experiment.cell_temperature10.0
experiment.exposure_time0.05
experiment.number_of_frames20
experiment.wavelength0.12
experiment.sample_detector_distance3.1
experiment.concentration_min0.3
experiment.concentration_max2.9
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.054
experiment.s_max3.495
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[]
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionnull
i0_calibration_standardnull
descriptionnull
experiment_descriptionnull
tags[]
intensity_unitnull
experimental_mw49.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i01450.0
pddf_i0_errornull
guinier_i01370.0
guinier_i0_errornull
pddf_rg5.1
pddf_rg_errornull
guinier_rg5.1
guinier_rg_errornull
pddf_dmax17.0
pddf_dmax_errornull
porod_volume120.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first12
guinier_point_last80
pddf_point_first12
pddf_point_last1200
i0_calibration_standard_datanull
intensities_log_log_plotSASDA76_datloglog_img.png
symmetrynull
last_modified2023-06-21T07:56:39.492710+02:00
bragg_peak[]
manifest.json:36 个字段值
字段路径原始值
codeSASDA76
statussuccess
started_at2026-08-11T15:03:00.818967+00:00
finished_at2026-08-11T15:03:09.044479+00:00
source_last_modified2023-06-21T07:56:39.492710+02:00
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查看完整 summary.json 原文
{
  "code": "SASDA76",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "The crystal structure of netrin-1 in complex with DCC reveals the bifunctionality of netrin-1 as a guidance cue.",
    "publication": {
      "title": "The crystal structure of netrin-1 in complex with DCC reveals the bifunctionality of netrin-1 as a guidance cue.",
      "author_list": "Finci LI, Krüger N, Sun X, Zhang J, Chegkazi M, Wu Y, Schenk G, Mertens HDT, Svergun DI, Zhang Y, Wang JH, Meijers R",
      "journal": "Neuron",
      "doi": "10.1016/j.neuron.2014.07.010",
      "pmid": "25123307",
      "published_date": "2014 Aug 20"
    },
    "status": "released",
    "submitted_date": null,
    "released_date": "2015-07-07"
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        "name": "Pilatus 2M",
        "resolution": null
      },
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      "city": "DESY; Hamburg",
      "country": "Germany",
      "beamline_name": "EMBL P12",
      "beam_geometry": null,
      "type_of_source": "X-ray synchrotron",
      "point_source": null,
      "line_collimation": null,
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      "xray_energy": null,
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    },
    "sample": {
      "molecule": [
        {
          "long_name": "Netrin-1",
          "short_name": "NetrinVIV",
          "sequence": "GPGLSMFAGQAAQPDPCSDENGHPRRCIPDFVNAAFGKDVRVSSTCGRPPARYCVVSERGEERLRSCHLCNASDPKKAHPPAFLTDLNNPHNLTCWQSENYLQFPHNVTLTLSLGKKFEVTYVSLQFCSPRPESMAIYKSMDYGRTWVPFQFYSTQCRKMYNRPHRAPITKQNEQEAVCTDSHTDMRPLSGGLIAFSTLDGRPSAHDFDNSPVLQDWVTATDIRVAFSRLHTFGDENEDDSELARDSYFYAVSDLQVGGRCKCNGHAARCVRDRDDSLVCDCRHNTAGPECDRCKPFHYDRPWQRATAREANECVACNCNLHARRCRFNMELYKLSGRKSGGVCLNCRHNTAGRHCHYCKEGYYRDMGKPITHRKACKACDCHPVGAAGKTCNQTTGQCPCKDGVTGITCNRCAKGYQQSRSPIAPCIKELHHHHHH",
          "organism": "Homo sapiens",
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          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MMRAVWEALAALAAVACLVGAVRGGPGLSMFAGQAAQPDPCSDENGHPRRCIPDFVNAAF\nGKDVRVSSTCGRPPARYCVVSERGEERLRSCHLCNASDPKKAHPPAFLTDLNNPHNLTCW\nQSENYLQFPHNVTLTLSLGKKFEVTYVSLQFCSPRPESMAIYKSMDYGRTWVPFQFYSTQ\nCRKMYNRPHRAPITKQNEQEAVCTDSHTDMRPLSGGLIAFSTLDGRPSAHDFDNSPVLQD\nWVTATDIRVAFSRLHTFGDENEDDSELARDSYFYAVSDLQVGGRCKCNGHAARCVRDRDD\nSLVCDCRHNTAGPECDRCKPFHYDRPWQRATAREANECVACNCNLHARRCRFNMELYKLS\nGRKSGGVCLNCRHNTAGRHCHYCKEGYYRDMGKPITHRKACKACDCHPVGAAGKTCNQTT\nGQCPCKDGVTGITCNRCAKGYQQSRSPIAPCIKIPVAPPTTAASSVEEPEDCDSYCKASK\nGKLKINMKKYCKKDYAVQIHILKADKAGDWWKFTVNIISVYKQGTSRIRRGDQSLWIRSR\nDIACKCPKIKPLKKYLLLGNAEDSPDQSGIVADKSSLVIQWRDTWARRLRKFQQREKKGK\nCKKA",
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          "long_name": "Deleted in Colorectal Cancer (FN5 & FN6)",
          "short_name": "dcc56",
          "sequence": "MLPPVGVQAVALTHDAVRVSWADNSVPKNQKTSEVRLYTVRWRTSFSASAKYKSEDTTSLSYTATGLKPNTMYEFSVMVTKNRRSSTWSMTAHATTYEAAPTSAPKDLTVITREGKPRAVIVSWQPPLEANGKITAYILFYTLDKNIPIDDWIMETISGDRLTHQIMDLNLDTMYYFRIQARNSKGVGPLSDPILFRTLKLEVLFQGPGGHHHHHHGGWSHPQFEK",
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      "buffer": {
        "name": "25 MES mM 200 mM NaCl 50 mM Tris 0.2 M ammonium sulfate (NH4)2(SO4) 1mM calcium chloride CaCl2",
        "concentration_unit": "mM",
        "comment": "MES/TRIS",
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      "name": "NetrinVIV DCC56 complex",
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      "absorbption": null,
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      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": "EMBL-Hamburg",
            "address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
            "full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
            "webpage": "http://www.embl-hamburg.de/index.php"
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        "orcid": null
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    "concentration_method": null,
    "concentration_unit": null,
    "date": "2013-10-31",
    "storage_temperature": 10.0,
    "cell_temperature": 10.0,
    "exposure_time": 0.05,
    "number_of_frames": 20,
    "wavelength": 0.12,
    "sample_detector_distance": 3.1,
    "concentration_min": 0.3,
    "concentration_max": 2.9,
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    "flow_rate": null,
    "s_min": 0.054,
    "s_max": 3.495,
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  "fits": [],
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  "pddf_software_version": null,
  "i0_calibration_standard": null,
  "description": null,
  "experiment_description": null,
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  "pddf_point_last": 1200,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDA76_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2023-06-21T07:56:39.492710+02:00",
  "bragg_peak": []
}
查看完整 manifest.json 原文
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