SASDEC6

Adenylation Domain of DNA ligase A with NAD+

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Single concentration 最后更新:2021-05-18T08:48:35.422747+02:00
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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Adenylation Domain of DNA ligase A with NAD+

浓度— – 10.8 缓冲液 / pH50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol / 8.0
实验温度10.0 设备 / 束线CSIR-Central Drug Research Institute / Anton Paar SAXSpace
波长0.154 nm曝光1800.0 s × 3

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
DNA ligase A
查看序列
VSSPDADQTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVGGAGFATDFEPVDHLERMLSLDNAFTADELAAWAGRIHAEVGDAAHYLCELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLEVRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGFRPATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVKVDEVALQRRLGSTSRAPRWAIAYKYPPEHHHHHH
proteinMycobacterium tuberculosisP9WNV12–328monomer分子数 137.519 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
1922[3]0.10364–5.9999 1/nm含误差列缺失 010sasbdb/entries/c6/sasdec6/source/SASDEC6.dat
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2. SASBDB 报告的指标 Reported Results

指标方法数值误差单位
dmaxP(r)6.17—nm
i0Guinier599573.022300.0arbitrary
i0P(r)595300.0—arbitrary
mwExperimental38.0—kDa
mwPorod59.0—kDa
porod_volumePorod94.26—nm³
rgGuinier2.370.13nm
rgP(r)2.345—nm

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

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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50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol缓冲液浓度—
pH8.0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2018-10-06储存 / 测量温度4.0 / 10.0
曝光时间1800.0帧数3
波长0.154样品-探测器距离0.3
光源X-ray in house探测器Mythen2 R 1K
机构 / 束线CSIR-Central Drug Research Institute / Anton Paar SAXSpace · Lucknow, India
q 范围0.104 – 6.0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/c6/sasdec6/source/SASDEC6.zipdownloaded6949576e4e04568e77fb753157a8c70094a1347f48b26a3954ded7e328fd4ce28a328下载查看原文件源站
pddfsasbdb/entries/c6/sasdec6/source/SASDEC6.outdownloaded55793482322ee4254b7cf15791b92dfd9dcb0516faedd3c95140e7c2ab0d647205d40下载查看原文件源站
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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:179 个字段值
字段路径原始值
codeSASDEC6
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleSalt bridges at the subdomain interfaces of the adenylation domain and active-site residues of <i>Mycobacterium tuberculosis</i> NAD <sup>+</sup> -dependent DNA ligase A (MtbLigA) are important for the initial steps of nick-sealing activity
project.publication.titleSalt bridges at the subdomain interfaces of the adenylation domain and active-site residues of <i>Mycobacterium tuberculosis</i> NAD <sup>+</sup> -dependent DNA ligase A (MtbLigA) are important for the initial steps of nick-sealing activity
project.publication.author_listAfsar M, Shukla A, Kumar N, Ramachandran R
project.publication.journalActa Crystallographica Section D Structural Biology
project.publication.doi10.1107/S2059798321003107
project.publication.pmidnull
project.publication.published_date2021 May 14
project.statusreleased
project.submitted_date2019-09-05
project.released_date2021-05-18
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experiment.instrument.detector.typeHybrid Photon Counting (HPC)
experiment.instrument.detector.nameMythen2 R 1K
experiment.instrument.detector.resolutionnull
experiment.instrument.nameCSIR-Central Drug Research Institute
experiment.instrument.cityLucknow
experiment.instrument.countryIndia
experiment.instrument.beamline_nameAnton Paar SAXSpace
experiment.instrument.beam_geometrynull
experiment.instrument.type_of_sourceX-ray in house
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_nameDNA ligase A
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceVSSPDADQTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVGGAGFATDFEPVDHLERMLSLDNAFTADELAAWAGRIHAEVGDAAHYLCELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLEVRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGFRPATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVKVDEVALQRRLGSTSRAPRWAIAYKYPPEHHHHHH
experiment.sample.molecule[0].organismMycobacterium tuberculosis
experiment.sample.molecule[0].uniprot_codeP9WNV1
experiment.sample.molecule[0].uniprot_range_first2
experiment.sample.molecule[0].uniprot_range_last328
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMSSPDADQTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPE LRTPDSPTQLVGGAGFATDFEPVDHLERMLSLDNAFTADELAAWAGRIHAEVGDAAHYLC ELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLE VRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGH VEGFRPATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVK VDEVALQRRLGSTSRAPRWAIAYKYPPEEAQTKLLDIRVNVGRTGRITPFAFMTPVKVAG STVGQATLHNASEIKRKGVLIGDTVVIRKAGDVIPEVLGPVVELRDGSEREFIMPTTCPE CGSPLAPEKEGDADIRCPNARGCPGQLRERVFHVASRNGLDIEVLGYEAGVALLQAKVIA DEGELFALTERDLLRTDLFRTKAGELSANGKRLLVNLDKAKAAPLWRVLVALSIRHVGPT AARALATEFGSLDAIAAASTDQLAAVEGVGPTIAAAVTEWFAVDWHREIVDKWRAAGVRM VDERDESVPRTLAGLTIVVTGSLTGFSRDDAKEAIVARGGKAAGSVSKKTNYVVAGDSPG SKYDKAVELGVPILDEDGFRRLLADGPASRT
experiment.sample.molecule[0].mw37.519
experiment.sample.molecule[0].total_mw37.519
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.name50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph8.0
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameAdenylation Domain of DNA ligase A with NAD+
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].addressIndia
experiment.contributor[0].affiliation[0].full_nameCSIR - Central Drug Research Institute
experiment.contributor[0].affiliation[0].webpagehttps://cdri.res.in/
experiment.contributor[0].contributor_nameRavishankar
experiment.contributor[0].contributor_surnameRamachandran
experiment.contributor[0].orcid
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2018-10-06
experiment.storage_temperature4.0
experiment.cell_temperature10.0
experiment.exposure_time1800.0
experiment.number_of_frames3
experiment.wavelength0.154
experiment.sample_detector_distance0.3
experiment.concentration_minnull
experiment.concentration_max10.8
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.104
experiment.s_max6.0
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].p_value0.001009
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fits[1].softwareGASBOR
fits[1].chi_square_value0.29
fits[1].p_value6.2e-05
fits[1].fit_residual_plotSASDEC6_fit2_fitresiduals_img.png
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fits[1].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSAXS data from solutions of the adenylation Domain of DNA ligase A with NAD+, in 50 mM Tris-HCl, 200 mM NaCl, 2mM β-mercaptoethanol, pH 8 were collected on the Anton Paar SAXSpace instrument at the CSIR-Central Drug Research Institute storage ring (Lucknow, India) using a Hybrid Photon Counting (HPC) Mythen2 R 1K detector at a sample-detector distance of 0.3 m and at a wavelength of λ = 0.154 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 10.80 mg/ml was measured at 10°C. Three successive 1800 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_mw38.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw59.0
porod_mw_errornull
pddf_i0595300.0
pddf_i0_errornull
guinier_i0599573.0
guinier_i0_error22300.0
pddf_rg2.345
pddf_rg_errornull
guinier_rg2.37
guinier_rg_error0.13
pddf_dmax6.17
pddf_dmax_errornull
porod_volume94.26
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first26
guinier_point_last70
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDEC6_datloglog_img.png
symmetrynull
last_modified2021-05-18T08:48:35.422747+02:00
bragg_peak[]
manifest.json:36 个字段值
字段路径原始值
codeSASDEC6
statussuccess
started_at2026-08-11T16:31:34.972321+00:00
finished_at2026-08-11T16:31:44.175566+00:00
source_last_modified2021-05-18T08:48:35.422747+02:00
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查看完整 summary.json 原文
{
  "code": "SASDEC6",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Salt bridges at the subdomain interfaces of the adenylation domain and active-site residues of <i>Mycobacterium tuberculosis</i>\n              NAD <sup>+</sup>\n              -dependent DNA ligase A (MtbLigA) are important for the initial steps of nick-sealing activity",
    "publication": {
      "title": "Salt bridges at the subdomain interfaces of the adenylation domain and active-site residues of <i>Mycobacterium tuberculosis</i>\n              NAD <sup>+</sup>\n              -dependent DNA ligase A (MtbLigA) are important for the initial steps of nick-sealing activity",
      "author_list": "Afsar M, Shukla A, Kumar N, Ramachandran R",
      "journal": "Acta Crystallographica Section D Structural Biology",
      "doi": "10.1107/S2059798321003107",
      "pmid": null,
      "published_date": "2021 May 14"
    },
    "status": "released",
    "submitted_date": "2019-09-05",
    "released_date": "2021-05-18"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEC6.out",
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查看完整 manifest.json 原文
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