SASDBJ4

Wild-type LytA choline-binding domain

数据类型：SASBDB 实验数据 状态：Published 曲线类型：Single concentration 最后更新：2023-05-25T11:21:52.654103+02:00

The CBD of wt-LytA forms a dimer in solution, in line with results from the crystal structure.

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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Wild-type LytA choline-binding domain

浓度	0.7 – 6.92 mg/ml	缓冲液 / pH	20 mM Tris 150 mM NaCl 5 mM choline chloride 1 µM ZnCl2 / 7.5
实验温度	10.0	设备 / 束线	DORIS III, DESY / EMBL X33
波长	0.15 nm	曝光	15.0 s × 8

分子组分

组分	类型 / 物种	UniProt 与构建体	寡聚状态	分子量
Lytic Amidase choline-binding domain	proteinStreptococcus pneumoniae	—173–318	dimer分子数 2	17.3 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
1	2170[3]	0.0854979–6.03197 1/nm	含误差列缺失 0	47	sasbdb/entries/j4/sasdbj4/source/SASDBJ4.dat

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2. SASBDB 报告的指标 Reported Results

指标	方法	数值	误差	单位
dmax	P(r)	10.0	1.0	nm
i0	Guinier	29.84	—	—
i0	P(r)	27.65	—	—
mw	Experimental	31.0	3.0	kDa
mw	Guinier I(0)	31.0	—	kDa
mw	Porod	30.81	—	kDa
porod_volume	Porod	49.3	—	nm³
rg	Guinier	3.34	0.27	nm
rg	P(r)	3.096	—	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

拟合 1 · —

χ²：2.7556CorMap p：3.1e-05单位：1/A

拟合数据拟合图

模型	名称 / 类型	软件	对称性	模型 MW	PDB 声明	来源文件
1	—atomic	SASREF 7	P2	34.58	—	模型图片

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4. 来源文件索引 Source Files

类别	路径	下载状态	大小
curve	sasbdb/entries/j4/sasdbj4/source/SASDBJ4.dat	downloaded	99896
full_entry_zip	sasbdb/entries/j4/sasdbj4/source/SASDBJ4.zip	downloaded	116044
pddf	sasbdb/entries/j4/sasdbj4/source/SASDBJ4.out	downloaded	99056
sascif	sasbdb/entries/j4/sasdbj4/source/SASDBJ4.sascif	downloaded	481319
summary	sasbdb/entries/j4/sasdbj4/source/summary.json	downloaded	6607

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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	20 mM Tris 150 mM NaCl 5 mM choline chloride 1 µM ZnCl2	缓冲液浓度	20.0 mM
pH	7.5	添加剂	150 mM NaCl, 5 mM choline chloride, 1 µM ZnCl2
缓冲液说明	with choline
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	False / —

采集条件与仪器

测量日期	2011-12-11	储存 / 测量温度	10.0 / 10.0
曝光时间	15.0	帧数	8
波长	0.15	样品-探测器距离	2.7
光源	X-ray synchrotron	探测器	Pilatus 1M-W
机构 / 束线	DORIS III, DESY / EMBL X33 · Hamburg, Germany
q 范围	0.085 – 6.032	样品体积 / 流速	— / —

SASBDB 原始图

可下载文件

类别	文件	状态	大小	校验值	下载与查看
curve	sasbdb/entries/j4/sasdbj4/source/SASDBJ4.dat	downloaded	99896	175067ec3476913ba152789b5c8ab5e8745cd43966bfc72f9f132f3eadaf6828	下载查看原文件源站
full_entry_zip	sasbdb/entries/j4/sasdbj4/source/SASDBJ4.zip	downloaded	116044	13277df6bb2ace4a78b957b536ecdbfa73491249b4ca91793d73b07edfc1a4cb	下载查看原文件源站
pddf	sasbdb/entries/j4/sasdbj4/source/SASDBJ4.out	downloaded	99056	9d807895f9664ea95791996bad09bb619c522e4500aea0ed72cc3bb285bd1bb4	下载查看原文件源站
sascif	sasbdb/entries/j4/sasdbj4/source/SASDBJ4.sascif	downloaded	481319	ae836a0ad3684279676ab77e6a620d52c9f15c6dc01f3b863a3ed394829ab0e5	下载查看原文件源站
summary	sasbdb/entries/j4/sasdbj4/source/summary.json	downloaded	6607	e96e2240d454a031fb2daa3e757698fc27b6a9479def671a8fbdcc9a82caf059	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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      "name": "SASDBJ4/pddf/SASDBJ4.out",
      "size": 99056
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    {
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      "name": "SASDBJ4/SASDBJ4_fit1.fit",
      "size": 46365
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      "name": "SASDBJ4/SASDBJ4_fit1_model1.pdb",
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pddf：来源记录

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  "size": 99056,
  "status": "downloaded",
  "url": "https://www.sasbdb.org/media/p_of_R_files/SASDBJ4.out"
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sascif：来源记录

{
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  "size": 481319,
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  "url": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBJ4.sascif"
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summary：来源记录

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  "status": "downloaded",
  "url": "https://www.sasbdb.org/rest-api/entry/summary/SASDBJ4/"
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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
code	SASDBJ4
status	Published
type_of_curve	Single concentration
angular_unit	1/nm
project.title	Structural and functional insights into peptidoglycan access for the lytic amidase LytA of Streptococcus pneumoniae.
project.publication.title	Structural and functional insights into peptidoglycan access for the lytic amidase LytA of Streptococcus pneumoniae.
project.publication.author_list	Mellroth P, Sandalova T, Kikhney A, Vilaplana F, Hesek D, Lee M, Mobashery S, Normark S, Svergun D, Henriques-Normark B, Achour A
project.publication.journal	MBio
project.publication.doi	10.1128/mBio.01120-13
project.publication.pmid	24520066
project.publication.published_date	2014 Feb 11
project.status	released
project.submitted_date	2014-02-11
project.released_date	2016-03-16
pddf_data	https://www.sasbdb.org/media/p_of_R_files/SASDBJ4.out
intensities_data	https://www.sasbdb.org/media/intensities_files/SASDBJ4.dat
intensities_log_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBJ4_dat_img.png
intensities_kratky_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBJ4_kratky_img.png
pddf_plot	https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBJ4_pofr_img.png
intensities_guinier_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBJ4_guinier_img.png
sascif_data	https://www.sasbdb.org/media/sascif/sascif_files/SASDBJ4.sascif
experiment.instrument.detector.type	Custom-built
experiment.instrument.detector.name	Pilatus 1M-W
experiment.instrument.detector.resolution	0.172
experiment.instrument.name	DORIS III, DESY
experiment.instrument.city	Hamburg
experiment.instrument.country	Germany
experiment.instrument.beamline_name	EMBL X33
experiment.instrument.beam_geometry	0.60
experiment.instrument.type_of_source	X-ray synchrotron
experiment.instrument.point_source	null
experiment.instrument.line_collimation	null
experiment.instrument.sample_path_length	null
experiment.instrument.line_collimation_slitlength	null
experiment.instrument.line_collimation_integrationwidth	null
experiment.instrument.xray_energy	null
experiment.instrument.beam_profile_ah	null
experiment.instrument.beam_profile_al	null
experiment.sample.molecule[0].long_name	Lytic Amidase choline-binding domain
experiment.sample.molecule[0].short_name	LytA CBD
experiment.sample.molecule[0].sequence	null
experiment.sample.molecule[0].organism	Streptococcus pneumoniae
experiment.sample.molecule[0].uniprot_code	null
experiment.sample.molecule[0].uniprot_range_first	173
experiment.sample.molecule[0].uniprot_range_last	318
experiment.sample.molecule[0].oligomerization	dimer
experiment.sample.molecule[0].molecular_type	protein
experiment.sample.molecule[0].uniprot_sequence	null
experiment.sample.molecule[0].mw	17.3
experiment.sample.molecule[0].total_mw	17.3
experiment.sample.molecule[0].number_molecules	2
experiment.sample.molecule[0].complex_state	False
experiment.sample.molecule[0].deuteration	null
experiment.sample.molecule[0].molecule_source	biological
experiment.sample.molecule[0].molecule_description	null
experiment.sample.buffer.name	20 mM Tris 150 mM NaCl 5 mM choline chloride 1 µM ZnCl2
experiment.sample.buffer.concentration_unit	mM
experiment.sample.buffer.comment	with choline
experiment.sample.buffer.additive	150 mM NaCl, 5 mM choline chloride, 1 µM ZnCl2
experiment.sample.buffer.concentration	20.0
experiment.sample.buffer.pka	null
experiment.sample.buffer.ph	7.5
experiment.sample.buffer.deuteration	null
experiment.sample.purity_method	null
experiment.sample.name	Wild-type LytA choline-binding domain
experiment.sample.ext_coefficient	null
experiment.sample.contrast	null
experiment.sample.specific_vol	null
experiment.sample.dry_vol	null
experiment.sample.absorbption	null
experiment.sample.deuteration	null
experiment.sample.mixture	False
experiment.contributor[0].affiliation[0].short_name	EMBL-Hamburg
experiment.contributor[0].affiliation[0].address	Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany
experiment.contributor[0].affiliation[0].full_name	European Molecular Biology Laboratory (EMBL) - Hamburg outstation
experiment.contributor[0].affiliation[0].webpage	http://www.embl-hamburg.de/index.php
experiment.contributor[0].contributor_name	Al
experiment.contributor[0].contributor_surname	Kikhney
experiment.contributor[0].orcid	https://orcid.org/0000-0003-1321-3956
experiment.concentration_method	null
experiment.concentration_unit	mg/ml
experiment.date	2011-12-11
experiment.storage_temperature	10.0
experiment.cell_temperature	10.0
experiment.exposure_time	15.0
experiment.number_of_frames	8
experiment.wavelength	0.15
experiment.sample_detector_distance	2.7
experiment.concentration_min	0.7
experiment.concentration_max	6.92
experiment.sample_volume	null
experiment.flow_rate	null
experiment.s_min	0.085
experiment.s_max	6.032
experiment.total_exposure_time	null
experiment.seccolumn	null
fits[0].models[0].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDBJ4_fit1_model1_img.png
fits[0].models[0].software	SASREF
fits[0].models[0].pdb_link	[]
fits[0].models[0].model_title	null
fits[0].models[0].type_of_model	atomic
fits[0].models[0].software_version	7
fits[0].models[0].model_data	https://www.sasbdb.org/media/pdb_file/SASDBJ4_fit1_model1.pdb
fits[0].models[0].model_mw	34.58
fits[0].models[0].bead_radius	null
fits[0].models[0].log	null
fits[0].models[0].symmetry	P2
fits[0].models[0].comment
fits[0].models[0].user	4
fits[0].fit_unit	1/A
fits[0].fit_plot	https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBJ4_fit1_fit_img.png
fits[0].software	null
fits[0].chi_square_value	2.7556
fits[0].p_value	3.1e-05
fits[0].fit_residual_plot	null
fits[0].fit_data	https://www.sasbdb.org/media/fitting_files/SASDBJ4_fit1.fit
fits[0].fit_log	null
fits[0].software_version	null
fits[0].description	null
estimated_volume_method	null
pddf_software	ATSAS GNOM
pddf_software_version	GNOM 5
i0_calibration_standard	BSA
description	The CBD of wt-LytA forms a dimer in solution, in line with results from the crystal structure.
experiment_description	null
tags[0]	X33
intensity_unit	null
experimental_mw	31.0
experimental_mw_error	3.0
guinier_i0_mw	31.0
guinier_i0_mw_error	null
porod_mw	30.81
porod_mw_error	null
pddf_i0	27.65
pddf_i0_error	null
guinier_i0	29.84
guinier_i0_error	null
pddf_rg	3.096
pddf_rg_error	null
guinier_rg	3.34
guinier_rg_error	0.27
pddf_dmax	10.0
pddf_dmax_error	1.0
porod_volume	49.3
porod_volume_error	null
estimated_volume	null
estimated_volume_error	null
guinier_point_first	27
guinier_point_last	112
pddf_point_first	34
pddf_point_last	1152
i0_calibration_standard_data	null
intensities_log_log_plot	SASDBJ4_datloglog_img.png
symmetry	null
last_modified	2023-05-25T11:21:52.654103+02:00
bragg_peak	[]

manifest.json：36 个字段值

字段路径	原始值
code	SASDBJ4
status	success
started_at	2026-08-11T14:24:29.732050+00:00
finished_at	2026-08-11T14:24:39.588962+00:00
source_last_modified	2023-05-25T11:21:52.654103+02:00
files[0].status	downloaded
files[0].url	https://www.sasbdb.org/rest-api/entry/summary/SASDBJ4/
files[0].path	/data/saxsdb/sasbdb/entries/j4/sasdbj4/source/summary.json
files[0].size	6607
files[0].sha256	e96e2240d454a031fb2daa3e757698fc27b6a9479def671a8fbdcc9a82caf059
files[1].status	downloaded
files[1].url	https://www.sasbdb.org/media/intensities_files/SASDBJ4.dat
files[1].path	/data/saxsdb/sasbdb/entries/j4/sasdbj4/source/SASDBJ4.dat
files[1].size	99896
files[1].sha256	175067ec3476913ba152789b5c8ab5e8745cd43966bfc72f9f132f3eadaf6828
files[1].role	curve
files[2].status	downloaded
files[2].url	https://www.sasbdb.org/media/p_of_R_files/SASDBJ4.out
files[2].path	/data/saxsdb/sasbdb/entries/j4/sasdbj4/source/SASDBJ4.out
files[2].size	99056
files[2].sha256	9d807895f9664ea95791996bad09bb619c522e4500aea0ed72cc3bb285bd1bb4
files[2].role	pddf
files[3].status	downloaded
files[3].url	https://www.sasbdb.org/media/sascif/sascif_files/SASDBJ4.sascif
files[3].path	/data/saxsdb/sasbdb/entries/j4/sasdbj4/source/SASDBJ4.sascif
files[3].size	481319
files[3].sha256	ae836a0ad3684279676ab77e6a620d52c9f15c6dc01f3b863a3ed394829ab0e5
files[3].role	sascif
files[4].status	downloaded
files[4].url	https://www.sasbdb.org/media/zip_directories/SASDBJ4.zip
files[4].path	/data/saxsdb/sasbdb/entries/j4/sasdbj4/source/SASDBJ4.zip
files[4].size	116044
files[4].sha256	13277df6bb2ace4a78b957b536ecdbfa73491249b4ca91793d73b07edfc1a4cb
files[4].role	full_entry_zip
files[4].zip_member_count	4
files[4].zip_validation	central_directory_readable

查看完整 summary.json 原文

{
  "code": "SASDBJ4",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Structural and functional insights into peptidoglycan access for the lytic amidase LytA of Streptococcus pneumoniae.",
    "publication": {
      "title": "Structural and functional insights into peptidoglycan access for the lytic amidase LytA of Streptococcus pneumoniae.",
      "author_list": "Mellroth P, Sandalova T, Kikhney A, Vilaplana F, Hesek D, Lee M, Mobashery S, Normark S, Svergun D, Henriques-Normark B, Achour A",
      "journal": "MBio",
      "doi": "10.1128/mBio.01120-13",
      "pmid": "24520066",
      "published_date": "2014 Feb 11"
    },
    "status": "released",
    "submitted_date": "2014-02-11",
    "released_date": "2016-03-16"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBJ4.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBJ4.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBJ4_dat_img.png",
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  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBJ4_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBJ4_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBJ4.sascif",
  "experiment": {
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        "name": "Pilatus 1M-W",
        "resolution": 0.172
      },
      "name": "DORIS III, DESY",
      "city": "Hamburg",
      "country": "Germany",
      "beamline_name": "EMBL X33",
      "beam_geometry": "0.60",
      "type_of_source": "X-ray synchrotron",
      "point_source": null,
      "line_collimation": null,
      "sample_path_length": null,
      "line_collimation_slitlength": null,
      "line_collimation_integrationwidth": null,
      "xray_energy": null,
      "beam_profile_ah": null,
      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
        {
          "long_name": "Lytic Amidase choline-binding domain",
          "short_name": "LytA CBD",
          "sequence": null,
          "organism": "Streptococcus pneumoniae",
          "uniprot_code": null,
          "uniprot_range_first": 173,
          "uniprot_range_last": 318,
          "oligomerization": "dimer",
          "molecular_type": "protein",
          "uniprot_sequence": null,
          "mw": 17.3,
          "total_mw": 17.3,
          "number_molecules": 2,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "20 mM Tris 150 mM NaCl 5 mM choline chloride 1 µM ZnCl2",
        "concentration_unit": "mM",
        "comment": "with choline",
        "additive": "150 mM NaCl, 5 mM choline chloride, 1 µM ZnCl2",
        "concentration": 20.0,
        "pka": null,
        "ph": 7.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Wild-type LytA choline-binding domain",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": false
    },
    "contributor": [
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        "affiliation": [
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查看完整 manifest.json 原文

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标题	Structural and functional insights into peptidoglycan access for the lytic amidase LytA of Streptococcus pneumoniae.
作者	Mellroth P, Sandalova T, Kikhney A, Vilaplana F, Hesek D, Lee M, Mobashery S, Normark S, Svergun D, Henriques-Normark B, Achour A
DOI / PMID	10.1128/mBio.01120-13 / 24520066