1r4q

Shiga toxin

Method: X-RAY DIFFRACTION D_max: 140.4 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	1r4q
沉积日期 deposition_date	2003-10-07
结构标题 title	Shiga toxin
关键词 keywords	AB5 toxin, 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	38.18 Å
回转半径 Rg (电子) rg_electron	38.41 Å
零角强度 I(0) i0	297045000.00
分子量 molecular_weight	137750.0 kDa
排除体积 excluded_volume	171490 Å³
包络体积 envelope_volume	214980 Å³
水化壳体积 shell_volume	50411 Å³
包络直径 envelope_diameter	150.2 Å
壳层 Rg shell_rg	40.68 Å
包络 Rg envelope_rg	38.58 Å
形状 Rg shape_rg	38.41 Å
总 Rg total_rg	38.56 Å
总原子数 total_atoms	9679
残基数 n_residues	1243
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	140.4 Å
Rg (实空间) rg_real	38.71 Å
Rg 误差 (实空间) rg_real_error	1.62 Å
I(0) (实空间) i0_real	2.9700e+08
I(0) 误差 (实空间) i0_real_error	5.4160e+06
Rg (倒空间) rg_reciprocal	38.38 Å
I(0) (倒空间) i0_reciprocal	296900000.0000
解质量估计 total_estimate	0.7831
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	37.7 Å
偏度 Skewness skewness	0.753
峰度 Kurtosis kurtosis	0.364
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	60540000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.556; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.841; Smooth: 0.667

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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	SHT cytotoxin A subunit
分子量 formula_weight	32264.4 kDa
EC 编号 ec_number	3.2.2.22
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,L
原子数 atom_count	9725

KEFTLDFSTAKTYVDSLNVIRSAIGTPLQTISSGGTSLLMIDSGTGDNLFAVDVRGIDPEEGRFNNLRLIVERNNLYVTGFVNRTNNVFYRFADFSHVTFPGTTAVTLSGDSSYTTLQRVAGISRTGMQINRHSLTTSYLDLMSHSGTSLTQSVARAMLRFVTVTAEALRFRQIQRGFRTTLDDLSGRSYVMTAEDVDLTLNWGRLSSVLPDYHGQDSVRVGRISFGSINAILGSVALILNCHHHASRVARMASDEFPSMCPADGRVRGITHNKILWDSSTLGAILMRRTISS

来源 Source

来源生物 organism	Shigella dysenteriae
NCBI 分类编号 ncbi_taxonomy_id	622
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Shigella toxin chain B
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	B,C,D,E,F,G,H,I,J,K

TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR

来源 Source

来源生物 organism	Shigella dysenteriae
NCBI 分类编号 ncbi_taxonomy_id	622
宿主生物 host_organism	Escherichia coli

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	46

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6. 折叠分类 (SCOP + CATH) 26 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1r4qa_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.165 — Ribosome inactivating proteins (RIP)
超家族 Superfamily superfamily	d.165.1 — Ribosome inactivating proteins (RIP)
家族 Family family	d.165.1.2 — Shiga toxin, A-chain

结构域编号 domain_id	d1r4qb_
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	d1r4qc_
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	d1r4qd_
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	d1r4qe_
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	d1r4qf_
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	d1r4qg_
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	d1r4qh_
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	d1r4qi_
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	d1r4qj_
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	d1r4qk_
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	d1r4ql_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.165 — Ribosome inactivating proteins (RIP)
超家族 Superfamily superfamily	d.165.1 — Ribosome inactivating proteins (RIP)
家族 Family family	d.165.1.2 — Shiga toxin, A-chain

CATH v4.4 (14 domains)

结构域编号 domain_id	1r4qA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	420 — Ricin (A subunit); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Ricin (A subunit), domain 1

结构域编号 domain_id	1r4qA02
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	470 — Ricin (A Subunit), domain 2
同源超家族 H-superfamily homologous superfamily	10 — Ricin (A Subunit), domain 2

结构域编号 domain_id	1r4qB00
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	1r4qC00
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	1r4qD00
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	1r4qE00
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	1r4qF00
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	1r4qG00
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	1r4qH00
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	1r4qI00
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	1r4qJ00
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	1r4qK00
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	1r4qL01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	420 — Ricin (A subunit); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Ricin (A subunit), domain 1

结构域编号 domain_id	1r4qL02
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	470 — Ricin (A Subunit), domain 2
同源超家族 H-superfamily homologous superfamily	10 — Ricin (A Subunit), domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	133.000 Å
晶胞边长 b length_b	147.180 Å
晶胞边长 c length_c	82.850 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	40

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	98.600 Å
R 因子 r_factor	0.2020
R_work r_work	0.1994
R_free r_free	0.2566

fit	/app/data/saxs_computation/r4/1r4q/1r4q.fit
pddf	/app/data/pr_computation/r4/1r4q/1r4q.pr.out
profile	/app/data/saxs_computation/r4/1r4q/1r4q.dat

Shiga toxin

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 polymer

聚合体 Polymer

来源 Source

Entity 3 water

6. 折叠分类 (SCOP + CATH) 26 domains

SCOP 2.08 (12 domains)

CATH v4.4 (14 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)