1oqe

Crystal structure of sTALL-1 with BAFF-R

Method: X-RAY DIFFRACTION D_max: 144.9 Å Quality: REASONABLE

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	1oqe
沉积日期 deposition_date	2003-03-07
结构标题 title	Crystal structure of sTALL-1 with BAFF-R
关键词 keywords	ligand receptor complex, IMMUNE SYSTEM; IMMUNE SYSTEM
实验方法 method	X-RAY DIFFRACTION

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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	44.18 Å
回转半径 Rg (电子) rg_electron	43.62 Å
零角强度 I(0) i0	484419000.00
分子量 molecular_weight	188380.0 kDa
排除体积 excluded_volume	238720 Å³
包络体积 envelope_volume	325720 Å³
水化壳体积 shell_volume	61525 Å³
包络直径 envelope_diameter	149.1 Å
壳层 Rg shell_rg	49.32 Å
包络 Rg envelope_rg	42.93 Å
形状 Rg shape_rg	43.58 Å
总 Rg total_rg	44.03 Å
总原子数 total_atoms	13240
残基数 n_residues	1681
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	144.9 Å
Rg (实空间) rg_real	44.19 Å
Rg 误差 (实空间) rg_real_error	1.14 Å
I(0) (实空间) i0_real	4.8440e+08
I(0) 误差 (实空间) i0_real_error	8.8470e+06
Rg (倒空间) rg_reciprocal	44.18 Å
I(0) (倒空间) i0_reciprocal	484400000.0000
解质量估计 total_estimate	0.6873
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	40.2 Å
偏度 Skewness skewness	0.215
峰度 Kurtosis kurtosis	-0.694
角度范围 angular_range	— – 0.1800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	129300000.0000
实空间数据点数 n_real_points	37
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 0.145; Positv: 1.000; Valcen: 0.961; Smooth: 0.847

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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 (2)

Entity 1 polymer

描述 description	Tumor necrosis factor ligand superfamily member 13B, soluble form
分子量 formula_weight	16244.6 kDa
来源方法 src_method	man
拷贝数 entity_count	10

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J
原子数 atom_count	13240

VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL

来源 Source

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

Entity 2 polymer

描述 description	Tumor necrosis factor receptor superfamily member 13C
分子量 formula_weight	3366.1 kDa
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	K,L,M,N,O,P,Q,R

PTPCVPAECFDLLVRHCVACGLLRTPRPKPA

来源 Source

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

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6. 折叠分类 (SCOP + CATH) 28 domains

SCOP 2.08 (18 domains)

结构域编号 domain_id	d1oqea_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.22 — TNF-like
超家族 Superfamily superfamily	b.22.1 — TNF-like
家族 Family family	b.22.1.1 — TNF-like

结构域编号 domain_id	d1oqeb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.22 — TNF-like
超家族 Superfamily superfamily	b.22.1 — TNF-like
家族 Family family	b.22.1.1 — TNF-like

结构域编号 domain_id	d1oqec_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.22 — TNF-like
超家族 Superfamily superfamily	b.22.1 — TNF-like
家族 Family family	b.22.1.1 — TNF-like

结构域编号 domain_id	d1oqed_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.22 — TNF-like
超家族 Superfamily superfamily	b.22.1 — TNF-like
家族 Family family	b.22.1.1 — TNF-like

结构域编号 domain_id	d1oqee_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.22 — TNF-like
超家族 Superfamily superfamily	b.22.1 — TNF-like
家族 Family family	b.22.1.1 — TNF-like

结构域编号 domain_id	d1oqef_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.22 — TNF-like
超家族 Superfamily superfamily	b.22.1 — TNF-like
家族 Family family	b.22.1.1 — TNF-like

结构域编号 domain_id	d1oqeg_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.22 — TNF-like
超家族 Superfamily superfamily	b.22.1 — TNF-like
家族 Family family	b.22.1.1 — TNF-like

结构域编号 domain_id	d1oqeh_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.22 — TNF-like
超家族 Superfamily superfamily	b.22.1 — TNF-like
家族 Family family	b.22.1.1 — TNF-like

结构域编号 domain_id	d1oqei_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.22 — TNF-like
超家族 Superfamily superfamily	b.22.1 — TNF-like
家族 Family family	b.22.1.1 — TNF-like

结构域编号 domain_id	d1oqej_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.22 — TNF-like
超家族 Superfamily superfamily	b.22.1 — TNF-like
家族 Family family	b.22.1.1 — TNF-like

结构域编号 domain_id	d1oqek_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.24 — TNF receptor-like
超家族 Superfamily superfamily	g.24.1 — TNF receptor-like
家族 Family family	g.24.1.2 — BAFF receptor-like

结构域编号 domain_id	d1oqel_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.24 — TNF receptor-like
超家族 Superfamily superfamily	g.24.1 — TNF receptor-like
家族 Family family	g.24.1.2 — BAFF receptor-like

结构域编号 domain_id	d1oqem_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.24 — TNF receptor-like
超家族 Superfamily superfamily	g.24.1 — TNF receptor-like
家族 Family family	g.24.1.2 — BAFF receptor-like

结构域编号 domain_id	d1oqen_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.24 — TNF receptor-like
超家族 Superfamily superfamily	g.24.1 — TNF receptor-like
家族 Family family	g.24.1.2 — BAFF receptor-like

结构域编号 domain_id	d1oqeo_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.24 — TNF receptor-like
超家族 Superfamily superfamily	g.24.1 — TNF receptor-like
家族 Family family	g.24.1.2 — BAFF receptor-like

结构域编号 domain_id	d1oqep_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.24 — TNF receptor-like
超家族 Superfamily superfamily	g.24.1 — TNF receptor-like
家族 Family family	g.24.1.2 — BAFF receptor-like

结构域编号 domain_id	d1oqeq_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.24 — TNF receptor-like
超家族 Superfamily superfamily	g.24.1 — TNF receptor-like
家族 Family family	g.24.1.2 — BAFF receptor-like

结构域编号 domain_id	d1oqer_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.24 — TNF receptor-like
超家族 Superfamily superfamily	g.24.1 — TNF receptor-like
家族 Family family	g.24.1.2 — BAFF receptor-like

CATH v4.4 (10 domains)

结构域编号 domain_id	1oqeA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1oqeB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1oqeC00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1oqeD00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1oqeE00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1oqeF00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1oqeG00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1oqeH00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1oqeI00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1oqeJ00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	40 —

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7. 引用文献 (1)

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晶胞边长 a length_a	233.261 Å
晶胞边长 b length_b	233.261 Å
晶胞边长 c length_c	211.286 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	120.00 °
晶胞分子数 Z z_pdb	120

空间群 space_group	P 63 2 2
空间群编号 int_tables_number	182
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2640
R_work r_work	0.2440
R_free r_free	0.2590

fit	/app/data/saxs_computation/oq/1oqe/1oqe.fit
pddf	/app/data/pr_computation/oq/1oqe/1oqe.pr.out
profile	/app/data/saxs_computation/oq/1oqe/1oqe.dat

Crystal structure of sTALL-1 with BAFF-R

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

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 28 domains

SCOP 2.08 (18 domains)

CATH v4.4 (10 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)