SASDXR8

Repeats-in-toxin domain Block V of Bifunctional hemolysin/adenylate cyclase, 10 mM MgCl2

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Single concentration 最后更新:2025-10-16T14:20:01.133964+02:00

1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Repeats-in-toxin domain Block V of Bifunctional hemolysin/adenylate cyclase, 10 mM MgCl2

浓度— – 10.0 缓冲液 / pH50 mM Tris, 5 mM DTT, 10 mM MgCl2 / 7.5
实验温度21.9 设备 / 束线Stanford Synchrotron Radiation Lightsource (SSRL) / BL4-2
波长0.1127 nm曝光2.0 s × 1

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
Repeats-in-toxin domain Block V of adenylate cyclase toxin
查看序列
MRGSHHHHHHGSHMELGASGSARDDVLIGDAGANVLNGLAGNDVLSGGAGDDVLLGDEGSDLLSGDAGNDDLFGGQGDDTYLFGVGYGHDTIYESGGGHDTIRINAGADQLWFARQGNDLEIRILGTDDALTVHDWYRDADHRVEIIHAANQAVDQAGIEKLVEAMAQYPDEFTSLEKLN*
proteinBordetella pertussisP0DKX71529–1680monomer分子数 119.1 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
1941[3]0.006551351–0.5025324 1/A含误差列缺失 02sasbdb/entries/r8/sasdxr8/source/SASDXR8.dat

2. SASBDB 报告的指标 Reported Results

指标方法数值误差单位
dmaxP(r)16.3Å
i0Guinier156.391arbitrary
i0P(r)157.4arbitrary
mwExperimental36900.0kDa
mwPorod38.0kDa
porod_volumePorod61.2ų
rgGuinier3.8090.145Å
rgP(r)3.98Å

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 · DENSS

χ²:1.6116CorMap 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
1densityDENSS 模型

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50 mM Tris, 5 mM DTT, 10 mM MgCl2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2024-08-01储存 / 测量温度23.0 / 21.9
曝光时间2.0帧数1
波长0.1127样品-探测器距离1.7
光源X-ray synchrotron探测器Pilatus3 X 1M
机构 / 束线Stanford Synchrotron Radiation Lightsource (SSRL) / BL4-2 · Menlo Park, CA, USA
q 范围0.066 – 5.025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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sascifsasbdb/entries/r8/sasdxr8/source/SASDXR8.sascifnot_available下载查看原文件源站
summarysasbdb/entries/r8/sasdxr8/source/summary.jsondownloaded89671f8743576a8634e865a27d46f7e5e64390ee0cb900a951ec5ac707710d77724a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:156 个字段值
字段路径原始值
codeSASDXR8
statusPublished
type_of_curveSingle concentration
angular_unit1/A
project.titleIon-selective conformational stabilization of a disordered repeats-in-toxin protein domain.
project.publication.titleIon-selective conformational stabilization of a disordered repeats-in-toxin protein domain.
project.publication.author_listGudinas AP, Shambharkar GM, Chang MP, Fernández D, Matsui T, Mai DJ
project.publication.journalBiophys J
project.publication.doi10.1016/j.bpj.2025.10.014
project.publication.pmid41088755
project.publication.published_date2025 Oct 13
project.statusreleased
project.submitted_date2025-09-05
project.released_date2025-10-16
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experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus3 X 1M
experiment.instrument.detector.resolution0.172
experiment.instrument.nameStanford Synchrotron Radiation Lightsource (SSRL)
experiment.instrument.cityMenlo Park, CA
experiment.instrument.countryUSA
experiment.instrument.beamline_nameBL4-2
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_nameRepeats-in-toxin domain Block V of adenylate cyclase toxin
experiment.sample.molecule[0].short_nameRTX Block V
experiment.sample.molecule[0].sequenceMRGSHHHHHHGSHMELGASGSARDDVLIGDAGANVLNGLAGNDVLSGGAGDDVLLGDEGSDLLSGDAGNDDLFGGQGDDTYLFGVGYGHDTIYESGGGHDTIRINAGADQLWFARQGNDLEIRILGTDDALTVHDWYRDADHRVEIIHAANQAVDQAGIEKLVEAMAQYPDEFTSLEKLN*
experiment.sample.molecule[0].organismBordetella pertussis
experiment.sample.molecule[0].uniprot_codeP0DKX7
experiment.sample.molecule[0].uniprot_range_first1529
experiment.sample.molecule[0].uniprot_range_last1680
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMQQSHQAGYANAADRESGIPAAVLDGIKAVAKEKNATLMFRLVNPHSTSLIAEGVATKGL GVHAKSSDWGLQAGYIPVNPNLSKLFGRAPEVIARADNDVNSSLAHGHTAVDLTLSKERL DYLRQAGLVTGMADGVVASNHAGYEQFEFRVKETSDGRYAVQYRRKGGDDFEAVKVIGNA AGIPLTADIDMFAIMPHLSNFRDSARSSVTSGDSVTDYLARTRRAASEATGGLDRERIDL LWKIARAGARSAVGTEARRQFRYDGDMNIGVITDFELEVRNALNRRAHAVGAQDVVQHGT EQNNPFPEADEKIFVVSATGESQMLTRGQLKEYIGQQRGEGYVFYENRAYGVAGKSLFDD GLGAAPGVPSGRSKFSPDVLETVPASPGLRRPSLGAVERQDSGYDSLDGVGSRSFSLGEV SDMAAVEAAELEMTRQVLHAGARQDDAEPGVSGASAHWGQRALQGAQAVAAAQRLVHAIA LMTQFGRAGSTNTPQEAASLSAAVFGLGEASSAVAETVSGFFRGSSRWAGGFGVAGGAMA LGGGIAAAVGAGMSLTDDAPAGQKAAAGAEIALQLTGGTVELASSIALALAAARGVTSGL QVAGASAGAAAGALAAALSPMEIYGLVQQSHYADQLDKLAQESSAYGYEGDALLAQLYRD KTAAEGAVAGVSAVLSTVGAAVSIAAAASVVGAPVAVVTSLLTGALNGILRGVQQPIIEK LANDYARKIDELGGPQAYFEKNLQARHEQLANSDGLRKMLADLQAGWNASSVIGVQTTEI SKSALELAAITGNADNLKSVDVFVDRFVQGERVAGQPVVLDVAAGGIDIASRKGERPALT FITPLAAPGEEQRRRTKTGKSEFTTFVEIVGKQDRWRIRDGAADTTIDLAKVVSQLVDAN GVLKHSIKLDVIGGDGDDVVLANASRIHYDGGAGTNTVSYAALGRQDSITVSADGERFNV RKQLNNANVYREGVATQTTAYGKRTENVQYRHVELARVGQLVEVDTLEHVQHIIGGAGND SITGNAHDNFLAGGSGDDRLDGGAGNDTLVGGEGQNTVIGGAGDDVFLQDLGVWSNQLDG GAGVDTVKYNVHQPSEERLERMGDTGIHADLQKGTVEKWPALNLFSVDHVKNIENLHGSR LNDRIAGDDQDNELWGHDGNDTIRGRGGDDILRGGLGLDTLYGEDGNDIFLQDDETVSDD IDGGAGLDTVDYSAMIHPGRIVAPHEYGFGIEADLSREWVRKASALGVDYYDNVRNVENV IGTSMKDVLIGDAQANTLMGQGGDDTVRGGDGDDLLFGGDGNDMLYGDAGNDTLYGGLGD DTLEGGAGNDWFGQTQAREHDVLRGGDGVDTVDYSQTGAHAGIAAGRIGLGILADLGAGR VDKLGEAGSSAYDTVSGIENVVGTELADRITGDAQANVLRGAGGADVLAGGEGDDVLLGG DGDDQLSGDAGRDRLYGEAGDDWFFQDAANAGNLLDGGDGRDTVDFSGPGRGLDAGAKGV FLSLGKGFASLMDEPETSNVLRNIENAVGSARDDVLIGDAGANVLNGLAGNDVLSGGAGD DVLLGDEGSDLLSGDAGNDDLFGGQGDDTYLFGVGYGHDTIYESGGGHDTIRINAGADQL WFARQGNDLEIRILGTDDALTVHDWYRDADHRVEIIHAANQAVDQAGIEKLVEAMAQYPD PGAAAAAPPAARVPDTLMQSLAVNWR
experiment.sample.molecule[0].mw19.1
experiment.sample.molecule[0].total_mw19.1
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_description
experiment.sample.buffer.name50 mM Tris, 5 mM DTT, 10 mM MgCl2
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.nameRepeats-in-toxin domain Block V of Bifunctional hemolysin/adenylate cyclase, 10 mM MgCl2
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].addressStanford, California, USA
experiment.contributor[0].affiliation[0].full_nameStanford University
experiment.contributor[0].affiliation[0].webpagehttps://www.stanford.edu/
experiment.contributor[0].contributor_nameAlana
experiment.contributor[0].contributor_surnameGudinas
experiment.contributor[0].orcidhttps://orcid.org/0000-0003-2859-7868
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2024-08-01
experiment.storage_temperature23.0
experiment.cell_temperature21.9
experiment.exposure_time2.0
experiment.number_of_frames1
experiment.wavelength0.1127
experiment.sample_detector_distance1.7
experiment.concentration_minnull
experiment.concentration_max10.0
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.066
experiment.s_max5.025
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[0].models[0].model_plotnull
fits[0].models[0].softwareDENSS
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fits[0].models[0].user1267
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fits[0].softwareDENSS
fits[0].chi_square_value1.6116
fits[0].p_value0.0
fits[0].fit_residual_plotSASDXR8_fit1_fitresiduals_img.png
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fits[0].fit_lognull
fits[0].software_versionnull
fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionnull
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of Disordered repeats-in-toxin domain Block V of Bifunctional hemolysin/adenylate cyclase in 50 mM Tris, 5 mM DTT, pH 7.5 were collected on the BL4-2 beam line at the Stanford Synchrotron Radiation Lightsource (SSRL) storage ring (Menlo Park, CA, USA) using a Pilatus3 X 1M detector at a sample-detector distance of 1.7 m and at a wavelength of λ = 0.1127 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 10.00 mg/ml was measured at 21.9°C. 500 frames were collected with an exposure time of 2 seconds. 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_mw36900.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw38.0
porod_mw_errornull
pddf_i0157.4
pddf_i0_errornull
guinier_i0156.391
guinier_i0_errornull
pddf_rg3.98
pddf_rg_errornull
guinier_rg3.809
guinier_rg_error0.145
pddf_dmax16.3
pddf_dmax_errornull
porod_volume61.2
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first4
guinier_point_last43
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDXR8_datloglog_img.png
symmetrynull
last_modified2025-10-16T14:20:01.133964+02:00
bragg_peak[]
manifest.json:34 个字段值
字段路径原始值
codeSASDXR8
statussuccess
started_at2026-08-11T15:59:26.001459+00:00
finished_at2026-08-11T15:59:34.606114+00:00
source_last_modified2025-10-16T14:20:01.133964+02:00
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查看完整 summary.json 原文
{
  "code": "SASDXR8",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/A",
  "project": {
    "title": "Ion-selective conformational stabilization of a disordered repeats-in-toxin protein domain.",
    "publication": {
      "title": "Ion-selective conformational stabilization of a disordered repeats-in-toxin protein domain.",
      "author_list": "Gudinas AP, Shambharkar GM, Chang MP, Fernández D, Matsui T, Mai DJ",
      "journal": "Biophys J",
      "doi": "10.1016/j.bpj.2025.10.014",
      "pmid": "41088755",
      "published_date": "2025 Oct 13"
    },
    "status": "released",
    "submitted_date": "2025-09-05",
    "released_date": "2025-10-16"
  },
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      "country": "USA",
      "beamline_name": "BL4-2",
      "beam_geometry": null,
      "type_of_source": "X-ray synchrotron",
      "point_source": null,
      "line_collimation": null,
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      "line_collimation_integrationwidth": null,
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    },
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          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": ""
        }
      ],
      "buffer": {
        "name": "50 mM Tris, 5 mM DTT, 10 mM MgCl2",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Repeats-in-toxin domain Block V of Bifunctional hemolysin/adenylate cyclase, 10 mM MgCl2",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Stanford, California, USA",
            "full_name": "Stanford University",
            "webpage": "https://www.stanford.edu/"
          }
        ],
        "contributor_name": "Alana",
        "contributor_surname": "Gudinas",
        "orcid": "https://orcid.org/0000-0003-2859-7868"
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2024-08-01",
    "storage_temperature": 23.0,
    "cell_temperature": 21.9,
    "exposure_time": 2.0,
    "number_of_frames": 1,
    "wavelength": 0.1127,
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    "concentration_max": 10.0,
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          "software": "DENSS",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "density",
          "software_version": null,
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDXR8_fit1_model1.mrc",
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          "comment": null,
          "user": 1267
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      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDXR8_fit1_fixed_fit_img.png",
      "software": "DENSS",
      "chi_square_value": 1.6116,
      "p_value": 0.0,
      "fit_residual_plot": "SASDXR8_fit1_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDXR8_fit1.fit",
      "fit_log": null,
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  "description": null,
  "experiment_description": "Synchrotron SAXS data from solutions of Disordered repeats-in-toxin domain Block V of Bifunctional hemolysin/adenylate cyclase in 50 mM Tris, 5 mM DTT, pH 7.5 were collected on the BL4-2 beam line at the Stanford Synchrotron Radiation Lightsource (SSRL) storage ring (Menlo Park, CA, USA) using a Pilatus3 X 1M detector at a sample-detector distance of 1.7 m and at a wavelength of λ = 0.1127 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 10.00 mg/ml was measured at 21.9°C. 500 frames were collected with an exposure time of 2 seconds. 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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  "intensities_log_log_plot": "SASDXR8_datloglog_img.png",
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  "last_modified": "2025-10-16T14:20:01.133964+02:00",
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}
查看完整 manifest.json 原文
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