SAXSdb — 1jr0

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1jr0
沉积日期 deposition_date	2001-08-09
结构标题 title	CHOLERA TOXIN B-PENTAMER WITH LIGAND BMSC-0011
关键词 keywords	ENTEROTOXIN, RECEPTOR, B-PENTAMER, TOXIN; TOXIN
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	24.59 Å
回转半径 Rg (电子) rg_electron	23.27 Å
零角强度 I(0) i0	60694800.00
分子量 molecular_weight	60329.0 kDa
排除体积 excluded_volume	75278 Å³
包络体积 envelope_volume	86642 Å³
水化壳体积 shell_volume	29940 Å³
包络直径 envelope_diameter	70.0 Å
壳层 Rg shell_rg	30.97 Å
包络 Rg envelope_rg	23.04 Å
形状 Rg shape_rg	23.30 Å
总 Rg total_rg	23.97 Å
总原子数 total_atoms	4230
残基数 n_residues	515
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	71.3 Å
Rg (实空间) rg_real	24.39 Å
Rg 误差 (实空间) rg_real_error	0.31 Å
I(0) (实空间) i0_real	6.0690e+07
I(0) 误差 (实空间) i0_real_error	7.3770e+05
Rg (倒空间) rg_reciprocal	24.44 Å
I(0) (倒空间) i0_reciprocal	60700000.0000
解质量估计 total_estimate	0.9154
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	70.2 Å
偏度 Skewness skewness	0.059
峰度 Kurtosis kurtosis	-0.654
角度范围 angular_range	— – 0.3250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	23660000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.980; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.968

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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 (3)

Entity 1 polymer

描述 description	cholera toxin B subunit
分子量 formula_weight	11623.3 kDa
来源方法 src_method	man
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D,E,F,G,H
原子数 atom_count	5015

TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN

来源 Source

来源生物 organism	Vibrio cholerae
NCBI 分类编号 ncbi_taxonomy_id	666
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	(3-NITRO-5-(2-MORPHOLIN-4-YL-ETHYLAMINOCARBONYL)PHENYL)-GALACTOPYRANOSIDE
分子量 formula_weight	457.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 3 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	695

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6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d1jr0d_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.2 — Bacterial enterotoxins
家族 Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

结构域编号 domain_id	d1jr0e_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.2 — Bacterial enterotoxins
家族 Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

结构域编号 domain_id	d1jr0f_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.2 — Bacterial enterotoxins
家族 Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

结构域编号 domain_id	d1jr0g_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.2 — Bacterial enterotoxins
家族 Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

结构域编号 domain_id	d1jr0h_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.2 — Bacterial enterotoxins
家族 Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

CATH v4.4 (5 domains)

结构域编号 domain_id	1jr0D00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	110 —

结构域编号 domain_id	1jr0E00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	110 —

结构域编号 domain_id	1jr0F00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	110 —

结构域编号 domain_id	1jr0G00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	110 —

结构域编号 domain_id	1jr0H00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	110 —

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7. 引用文献 (1)

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晶胞边长 a length_a	102.098 Å
晶胞边长 b length_b	66.064 Å
晶胞边长 c length_c	78.565 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	105.74 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	20

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	1.300 Å
最低分辨率 resolution_low	22.000 Å
R 因子 r_factor	0.1307
R_work r_work	—
R_free r_free	0.1834

fit	/app/data/saxs_computation/jr/1jr0/1jr0.fit
pddf	/app/data/pr_computation/jr/1jr0/1jr0.pr.out
profile	/app/data/saxs_computation/jr/1jr0/1jr0.dat

CHOLERA TOXIN B-PENTAMER WITH LIGAND BMSC-0011

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 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

Entity 3 water

6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)