SASDBF4

Wild-type LytA (N-His6) with choline

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

The full-length LytA dimer adopts a rigid V-shaped scaffold with the two amidase domains in the trans configuration.

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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Wild-type LytA (N-His6) with choline

浓度	1.0 – 5.0 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 with choline	proteinStreptococcus pneumoniae	——–—	dimer分子数 2	37.4 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	2138[3]	0.176504–6.02412 1/nm	含误差列缺失 0	99	sasbdb/entries/f4/sasdbf4/source/SASDBF4.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)	15.0	1.5	nm
i0	Guinier	77.9	—	—
i0	P(r)	78.72	0.231	—
mw	Experimental	75.0	8.0	kDa
mw	Guinier I(0)	66.0	—	kDa
mw	Porod	72.0	7.0	kDa
porod_volume	Porod	115.2	—	nm³
rg	Guinier	4.85	0.5	nm
rg	P(r)	4.953	—	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 · —

χ²：2.111CorMap p：0.0单位：1/A

拟合数据拟合图残差图

模型	名称 / 类型	软件	对称性	模型 MW	PDB 声明	来源文件
1	—atomic	SASREF	P2	73.55	—	模型图片

拟合 2 · —

χ²：1.252161CorMap p：0.191444单位：1/A

拟合数据拟合图残差图

模型	名称 / 类型	软件	对称性	模型 MW	PDB 声明	来源文件
1	—dummy	DAMMIF r2835	P2	64.0	—	模型图片日志

▶

4. 来源文件索引 Source Files

类别	路径	下载状态	大小
curve	sasbdb/entries/f4/sasdbf4/source/SASDBF4.dat	downloaded	98603
full_entry_zip	sasbdb/entries/f4/sasdbf4/source/SASDBF4.zip	downloaded	158485
pddf	sasbdb/entries/f4/sasdbf4/source/SASDBF4.out	downloaded	58439
sascif	sasbdb/entries/f4/sasdbf4/source/SASDBF4.sascif	downloaded	834682
summary	sasbdb/entries/f4/sasdbf4/source/summary.json	downloaded	7715

▶

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	2011-07-02	储存 / 测量温度	— / 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	0.177 – 6.024	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/f4/sasdbf4/source/SASDBF4.dat	downloaded	98603	82f9e03aa653be136026935624ff9a9e0291f06161e479acd1531c8e56cb5160	下载查看原文件源站
full_entry_zip	sasbdb/entries/f4/sasdbf4/source/SASDBF4.zip	downloaded	158485	f94319d6e9a7e4aa37d0c4f6212ac8f4c25f15239edda828da689a575e304363	下载查看原文件源站
pddf	sasbdb/entries/f4/sasdbf4/source/SASDBF4.out	downloaded	58439	c6181f307c757218a251699368f0e2e9f86b01d46c410fc0d4b19c130b003d21	下载查看原文件源站
sascif	sasbdb/entries/f4/sasdbf4/source/SASDBF4.sascif	downloaded	834682	a3b793c137beb8a2a17b81f6de530e3bb98e7275af9239a110e66de25686f257	下载查看原文件源站
summary	sasbdb/entries/f4/sasdbf4/source/summary.json	downloaded	7715	4126e95f5aa048a168ce1f2e0aa064a8ef14851e0e55d98fd5dac685e8671c0e	下载查看原文件源站

curve：来源记录

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  "url": "https://www.sasbdb.org/media/intensities_files/SASDBF4.dat"
}

full_entry_zip：来源记录与 ZIP 内部目录（6 项）

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  "url": "https://www.sasbdb.org/media/zip_directories/SASDBF4.zip",
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    {
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      "name": "SASDBF4/SASDBF4_fit1.fit",
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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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  "status": "downloaded",
  "url": "https://www.sasbdb.org/rest-api/entry/summary/SASDBF4/"
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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
code	SASDBF4
status	Published
type_of_curve	Extrapolated to infinite dilution
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/SASDBF4.out
intensities_data	https://www.sasbdb.org/media/intensities_files/SASDBF4.dat
intensities_log_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBF4_dat_img.png
intensities_kratky_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBF4_kratky_img.png
pddf_plot	https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBF4_pofr_img.png
intensities_guinier_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBF4_guinier_img.png
sascif_data	https://www.sasbdb.org/media/sascif/sascif_files/SASDBF4.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 with choline
experiment.sample.molecule[0].short_name	wt-LytA-His6
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	null
experiment.sample.molecule[0].uniprot_range_last	null
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	37.4
experiment.sample.molecule[0].total_mw	74.8
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 (N-His6) with choline
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	2011-07-02
experiment.storage_temperature	null
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	1.0
experiment.concentration_max	5.0
experiment.sample_volume	null
experiment.flow_rate	null
experiment.s_min	0.177
experiment.s_max	6.024
experiment.total_exposure_time	null
experiment.seccolumn	null
fits[0].models[0].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDBF4_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
fits[0].models[0].model_data	https://www.sasbdb.org/media/pdb_file/SASDBF4_fit1_model1.pdb
fits[0].models[0].model_mw	73.55
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/SASDBF4_fit1_fit_img.png
fits[0].software	null
fits[0].chi_square_value	2.111
fits[0].p_value	0.0
fits[0].fit_residual_plot	SASDBF4_fit1_fitresiduals_img.png
fits[0].fit_data	https://www.sasbdb.org/media/fitting_files/SASDBF4_fit1.fit
fits[0].fit_log	null
fits[0].software_version	null
fits[0].description	null
fits[1].models[0].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDBF4_fit2_model1_img.png
fits[1].models[0].software	DAMMIF
fits[1].models[0].pdb_link	[]
fits[1].models[0].model_title	null
fits[1].models[0].type_of_model	dummy
fits[1].models[0].software_version	r2835
fits[1].models[0].model_data	https://www.sasbdb.org/media/pdb_file/SASDBF4_fit2_model1.pdb
fits[1].models[0].model_mw	64.0
fits[1].models[0].bead_radius	3.2
fits[1].models[0].log	https://www.sasbdb.org/media/log_files/lyta2u_5.log
fits[1].models[0].symmetry	P2
fits[1].models[0].comment
fits[1].models[0].user	4
fits[1].fit_unit	1/A
fits[1].fit_plot	https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBF4_fit2_fit_img.png
fits[1].software	null
fits[1].chi_square_value	1.252161
fits[1].p_value	0.191444
fits[1].fit_residual_plot	SASDBF4_fit2_fitresiduals_img.png
fits[1].fit_data	https://www.sasbdb.org/media/fitting_files/SASDBF4_fit2.fir
fits[1].fit_log	null
fits[1].software_version	null
fits[1].description	null
estimated_volume_method	null
pddf_software	ATSAS GNOM
pddf_software_version	GNOM 5
i0_calibration_standard	BSA
description	The full-length LytA dimer adopts a rigid V-shaped scaffold with the two amidase domains in the trans configuration.
experiment_description	null
tags[0]	X33
intensity_unit	null
experimental_mw	75.0
experimental_mw_error	8.0
guinier_i0_mw	66.0
guinier_i0_mw_error	null
porod_mw	72.0
porod_mw_error	7.0
pddf_i0	78.72
pddf_i0_error	0.231
guinier_i0	77.9
guinier_i0_error	null
pddf_rg	4.953
pddf_rg_error	null
guinier_rg	4.85
guinier_rg_error	0.5
pddf_dmax	15.0
pddf_dmax_error	1.5
porod_volume	115.2
porod_volume_error	null
estimated_volume	null
estimated_volume_error	null
guinier_point_first	1
guinier_point_last	31
pddf_point_first	1
pddf_point_last	614
i0_calibration_standard_data	null
intensities_log_log_plot	SASDBF4_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	SASDBF4
status	success
started_at	2026-08-11T14:22:19.444952+00:00
finished_at	2026-08-11T14:22:33.428791+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/SASDBF4/
files[0].path	/data/saxsdb/sasbdb/entries/f4/sasdbf4/source/summary.json
files[0].size	7715
files[0].sha256	4126e95f5aa048a168ce1f2e0aa064a8ef14851e0e55d98fd5dac685e8671c0e
files[1].status	downloaded
files[1].url	https://www.sasbdb.org/media/intensities_files/SASDBF4.dat
files[1].path	/data/saxsdb/sasbdb/entries/f4/sasdbf4/source/SASDBF4.dat
files[1].size	98603
files[1].sha256	82f9e03aa653be136026935624ff9a9e0291f06161e479acd1531c8e56cb5160
files[1].role	curve
files[2].status	downloaded
files[2].url	https://www.sasbdb.org/media/p_of_R_files/SASDBF4.out
files[2].path	/data/saxsdb/sasbdb/entries/f4/sasdbf4/source/SASDBF4.out
files[2].size	58439
files[2].sha256	c6181f307c757218a251699368f0e2e9f86b01d46c410fc0d4b19c130b003d21
files[2].role	pddf
files[3].status	downloaded
files[3].url	https://www.sasbdb.org/media/sascif/sascif_files/SASDBF4.sascif
files[3].path	/data/saxsdb/sasbdb/entries/f4/sasdbf4/source/SASDBF4.sascif
files[3].size	834682
files[3].sha256	a3b793c137beb8a2a17b81f6de530e3bb98e7275af9239a110e66de25686f257
files[3].role	sascif
files[4].status	downloaded
files[4].url	https://www.sasbdb.org/media/zip_directories/SASDBF4.zip
files[4].path	/data/saxsdb/sasbdb/entries/f4/sasdbf4/source/SASDBF4.zip
files[4].size	158485
files[4].sha256	f94319d6e9a7e4aa37d0c4f6212ac8f4c25f15239edda828da689a575e304363
files[4].role	full_entry_zip
files[4].zip_member_count	6
files[4].zip_validation	central_directory_readable

查看完整 summary.json 原文

{
  "code": "SASDBF4",
  "status": "Published",
  "type_of_curve": "Extrapolated to infinite dilution",
  "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/SASDBF4.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBF4.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBF4_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBF4_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBF4_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBF4_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBF4.sascif",
  "experiment": {
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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