1o7c

Solution structure of the human TSG-6 Link module in the presence of a hyaluronan octasaccharide

Method: SOLUTION NMR D_max: 42.1 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1o7c
沉积日期 deposition_date	2002-10-29
结构标题 title	Solution structure of the human TSG-6 Link module in the presence of a hyaluronan octasaccharide
关键词 keywords	HYALURONAN-BINDING DOMAIN, CARBOHYDRATE-BINDING DOMAIN, LINK MODULE, CELL ADHESION, GLYCOPROTEIN; CELL ADHESION
实验方法 method	SOLUTION NMR

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	12.71 Å
回转半径 Rg (电子) rg_electron	12.74 Å
零角强度 I(0) i0	672204000.00
分子量 molecular_weight	218690.0 kDa
排除体积 excluded_volume	273120 Å³
包络体积 envelope_volume	22327 Å³
水化壳体积 shell_volume	13063 Å³
包络直径 envelope_diameter	49.0 Å
壳层 Rg shell_rg	20.32 Å
包络 Rg envelope_rg	14.78 Å
形状 Rg shape_rg	12.71 Å
总 Rg total_rg	13.00 Å
总原子数 total_atoms	30580
残基数 n_residues	1960
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	42.1 Å
Rg (实空间) rg_real	12.63 Å
Rg 误差 (实空间) rg_real_error	0.26 Å
I(0) (实空间) i0_real	6.7220e+08
I(0) 误差 (实空间) i0_real_error	7.3230e+06
Rg (倒空间) rg_reciprocal	12.64 Å
I(0) (倒空间) i0_reciprocal	672200000.0000
解质量估计 total_estimate	0.8823
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	14.9 Å
偏度 Skewness skewness	0.088
峰度 Kurtosis kurtosis	-0.494
角度范围 angular_range	— – 0.5000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	270700.0000
实空间数据点数 n_real_points	80
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.996

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (1)

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6. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1o7ct_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.169 — C-type lectin-like
超家族 Superfamily superfamily	d.169.1 — C-type lectin-like
家族 Family family	d.169.1.4 — Link domain

CATH v4.4 (1 domains)

结构域编号 domain_id	1o7cT00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

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7. 引用文献 (10)

The link module from ovulation- and inflammation-associated protein TSG-6 changes conformation on hyaluronan binding.

J. Biol. Chem. (2003)

PMID: 12972412 · DOI: 10.1074/jbc.M309623200 PRIMARY

The Link Module from Human Tsg-6 Inhibits Neutrophil Migration in a Hyaluronan- and Inter-Alpha -Inhibitor-Independent Manner

J.Biol.Chem. (2002)

PMID: 12401803 · DOI: 10.1074/JBC.M205121200

Hyaluronan Binding Properties of a Cd44 Chimera Containing the Link Module of Tsg-6

J.Biol.Chem. (2002)

PMID: 12011075 · DOI: 10.1074/JBC.M201068200

;Mapping the Hyaluronan-Binding Site on the Link Module from Human Tumor Necrosis Factor-Stimulated Gene-6 by Site-Directed Mutagenesis ;

J.Biol.Chem. (2001)

PMID: 11287417 · DOI: 10.1074/JBC.M100666200

Novel Methods for the Preparation and Characterization of Hyaluronan Oligosaccharides of Defined Length

Glycobiology (2001)

PMID: 11805075 · DOI: 10.1093/GLYCOB/11.12.1025

Localization and Characterization of the Hyaluronan-Binding Site on the Link Module from Human Tsg-6

Structure (2000)

PMID: 10903951 · DOI: 10.1016/S0969-2126(00)00163-5

Method for Quantitative Refolding of the Link Module from Human Tsg-6

Protein Expr.Purif. (1997)

PMID: 9126602 · DOI: 10.1006/PREP.1996.0694

;Overexpression, Purification, and Refolding of Link Module from Human Tsg-6 in Escherichia Coli: Effect of Temperature, Media, and Mutagenesis on Lysine Misincorporation at Arginine Aga Codons ;

Protein Expr.Purif. (1996)

PMID: 8812829 · DOI: 10.1006/PREP.1996.0068

Solution Structure of the Link Module: A Hyaluronan-Binding Domain Involved in Extracellular Matrix Stability and Cell Migration

Cell(Cambridge,Mass.) (1996)

PMID: 8797823 · DOI: 10.1016/S0092-8674(00)80151-8

;A Novel Secretory Tumour Necrosis Factor-Inducible Protein (Tsg-6) is a Member of the Family of Hyaluronate Binding Proteins, Closely Related to the Adhesion Receptor Cd44 ;

J.Cell Biol. (1992)

PMID: 1730767 · DOI: 10.1083/JCB.116.2.545

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	1

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

描述 description	TUMOR NECROSIS FACTOR-INDUCIBLE PROTEIN TSG-6
分子量 formula_weight	10946.6 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体类型 type	polypeptide(L)
链编号 strand_id	T
原子数 atom_count	30580

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI

Solution structure of the human TSG-6 Link module in the presence of a hyaluronan octasaccharide

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

5. 实体与聚合体信息 (1)

Entity 1 polymer

聚合体 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. 引用文献 (10)

8. 文件与曲线 (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/o7/1o7c/1o7c.fit
pddf	/app/data/pr_computation/o7/1o7c/1o7c.pr.out
profile	/app/data/saxs_computation/o7/1o7c/1o7c.dat