2c5c

Shiga-like toxin 1 B subunit complexed with a bivalent inhibitor

Method: X-RAY DIFFRACTION D_max: 96.2 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	2c5c
沉积日期 deposition_date	2005-10-26
结构标题 title	Shiga-like toxin 1 B subunit complexed with a bivalent inhibitor
关键词 keywords	BACTERIAL EXOTOXIN, GB3 BINDING ACTIVITY, BIVALENT LIGAND, PROTEIN-CARBOHYDRATE RECOGNITION, OB FOLD, 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	29.94 Å
回转半径 Rg (电子) rg_electron	29.18 Å
零角强度 I(0) i0	123677000.00
分子量 molecular_weight	86559.0 kDa
排除体积 excluded_volume	107600 Å³
包络体积 envelope_volume	129640 Å³
水化壳体积 shell_volume	37246 Å³
包络直径 envelope_diameter	102.2 Å
壳层 Rg shell_rg	36.39 Å
包络 Rg envelope_rg	29.05 Å
形状 Rg shape_rg	29.12 Å
总 Rg total_rg	29.98 Å
总原子数 total_atoms	6050
残基数 n_residues	690
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	96.2 Å
Rg (实空间) rg_real	29.93 Å
Rg 误差 (实空间) rg_real_error	0.48 Å
I(0) (实空间) i0_real	1.2370e+08
I(0) 误差 (实空间) i0_real_error	1.7540e+06
Rg (倒空间) rg_reciprocal	29.94 Å
I(0) (倒空间) i0_reciprocal	123700000.0000
解质量估计 total_estimate	0.6713
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	36.3 Å
偏度 Skewness skewness	0.368
峰度 Kurtosis kurtosis	-0.289
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	19150000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.883; Stabil: 1.000; Sysdev: 0.050; Positv: 1.000; Valcen: 1.000; Smooth: 0.923

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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 (9)

Entity 1 polymer

描述 description	SHIGA-LIKE TOXIN 1 B SUBUNIT
分子量 formula_weight	7698.6 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	6136

TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR

来源 Source

来源生物 organism	BACTERIOPHAGE H30
NCBI 分类编号 ncbi_taxonomy_id	12371
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 branched

描述 description	alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose
分子量 formula_weight	504.4 kDa
来源方法 src_method	man
拷贝数 entity_count	10

Entity 3 branched

描述 description	alpha-D-galactopyranose-(1-4)-alpha-D-galactopyranose
分子量 formula_weight	342.3 kDa
来源方法 src_method	man
拷贝数 entity_count	6

Entity 4 branched

描述 description	alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
分子量 formula_weight	504.4 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 5 branched

描述 description	alpha-D-galactopyranose-(1-4)-alpha-D-galactopyranose-(1-4)-beta-D-glucopyranose
分子量 formula_weight	504.4 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 6 non-polymer

描述 description	DIETHYL PROPANE-1,3-DIYLBISCARBAMATE
分子量 formula_weight	218.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 7 non-polymer

描述 description	alpha-D-galactopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 8 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 9 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	18

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6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d2c5ca_
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	d2c5cb_
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	d2c5cc_
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	d2c5cd_
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	d2c5ce_
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	d2c5cf_
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	d2c5cg_
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	d2c5ch_
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	d2c5ci_
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	d2c5cj_
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 (10 domains)

结构域编号 domain_id	2c5cA00
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	70 —

结构域编号 domain_id	2c5cB00
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	70 —

结构域编号 domain_id	2c5cC00
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	70 —

结构域编号 domain_id	2c5cD00
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	70 —

结构域编号 domain_id	2c5cE00
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	70 —

结构域编号 domain_id	2c5cF00
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	70 —

结构域编号 domain_id	2c5cG00
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	70 —

结构域编号 domain_id	2c5cH00
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	70 —

结构域编号 domain_id	2c5cI00
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	70 —

结构域编号 domain_id	2c5cJ00
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	70 —

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7. 引用文献 (1)

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晶胞边长 a length_a	114.313 Å
晶胞边长 b length_b	114.313 Å
晶胞边长 c length_c	406.936 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	180

空间群 space_group	H 3 2
空间群编号 int_tables_number	155
晶系 crystal_system	—

分辨率 resolution	2.940 Å
最低分辨率 resolution_low	22.760 Å
R 因子 r_factor	0.2010
R_work r_work	0.1980
R_free r_free	0.2670

fit	/app/data/saxs_computation/c5/2c5c/2c5c.fit
pddf	/app/data/pr_computation/c5/2c5c/2c5c.pr.out
profile	/app/data/saxs_computation/c5/2c5c/2c5c.dat

Shiga-like toxin 1 B subunit complexed with a bivalent inhibitor

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 (9)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 branched

Entity 3 branched

Entity 4 branched

Entity 5 branched

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 water

6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)