2a6q

Crystal structure of YefM-YoeB complex

Method: X-RAY DIFFRACTION D_max: 74.2 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	2a6q
沉积日期 deposition_date	2005-07-04
结构标题 title	Crystal structure of YefM-YoeB complex
关键词 keywords	YoeB, YefM, toxin, antitoxin, addiction modules, RNase, inhibitor, TOXIN INHIBITOR-TOXIN COMPLEX; TOXIN INHIBITOR/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	23.67 Å
回转半径 Rg (电子) rg_electron	22.58 Å
零角强度 I(0) i0	48591200.00
分子量 molecular_weight	52640.0 kDa
排除体积 excluded_volume	65393 Å³
包络体积 envelope_volume	77570 Å³
水化壳体积 shell_volume	28121 Å³
包络直径 envelope_diameter	73.5 Å
壳层 Rg shell_rg	30.00 Å
包络 Rg envelope_rg	22.68 Å
形状 Rg shape_rg	22.56 Å
总 Rg total_rg	23.49 Å
总原子数 total_atoms	3688
残基数 n_residues	456
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	74.2 Å
Rg (实空间) rg_real	23.50 Å
Rg 误差 (实空间) rg_real_error	0.29 Å
I(0) (实空间) i0_real	4.8590e+07
I(0) 误差 (实空间) i0_real_error	5.5090e+05
Rg (倒空间) rg_reciprocal	23.54 Å
I(0) (倒空间) i0_reciprocal	48590000.0000
解质量估计 total_estimate	0.7362
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	30.1 Å
偏度 Skewness skewness	0.085
峰度 Kurtosis kurtosis	-0.573
角度范围 angular_range	— – 0.3350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	22720000.0000
实空间数据点数 n_real_points	65
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 0.286; Positv: 1.000; Valcen: 0.993; Smooth: 0.999

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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	Antitoxin yefM
分子量 formula_weight	9610.9 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	3841

GPHMRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLLRSPANARRLMDSIDSLKSGKGTEKDIIE

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	Toxin yoeB
分子量 formula_weight	10233.7 kDa
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	E,F

MKLIWSEESWDDYLYWQETDKRIVKKINELIKDTRRTPFEGKGKPEPLKHNLSGFWSRRITEEHRLVYAVTDDSLLIAACRYHY

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli BL21(DE3)

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	153

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d2a6qa1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.306 — YefM-like
超家族 Superfamily superfamily	d.306.1 — YefM-like
家族 Family family	d.306.1.1 — YefM-like

结构域编号 domain_id	d2a6qa2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2a6qb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.306 — YefM-like
超家族 Superfamily superfamily	d.306.1 — YefM-like
家族 Family family	d.306.1.1 — YefM-like

结构域编号 domain_id	d2a6qb2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2a6qc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.306 — YefM-like
超家族 Superfamily superfamily	d.306.1 — YefM-like
家族 Family family	d.306.1.1 — YefM-like

结构域编号 domain_id	d2a6qc3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2a6qd2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.306 — YefM-like
超家族 Superfamily superfamily	d.306.1 — YefM-like
家族 Family family	d.306.1.1 — YefM-like

结构域编号 domain_id	d2a6qd3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2a6qe1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.298 — RelE-like
超家族 Superfamily superfamily	d.298.1 — RelE-like
家族 Family family	d.298.1.1 — YoeB/Txe-like

结构域编号 domain_id	d2a6qf_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.298 — RelE-like
超家族 Superfamily superfamily	d.298.1 — RelE-like
家族 Family family	d.298.1.1 — YoeB/Txe-like

CATH v4.4 (8 domains)

结构域编号 domain_id	2a6qA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1620 — YefM-like fold
同源超家族 H-superfamily homologous superfamily	10 — YefM-like domain

结构域编号 domain_id	2a6qA02
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	330 —

结构域编号 domain_id	2a6qB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1620 — YefM-like fold
同源超家族 H-superfamily homologous superfamily	10 — YefM-like domain

结构域编号 domain_id	2a6qC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1620 — YefM-like fold
同源超家族 H-superfamily homologous superfamily	10 — YefM-like domain

结构域编号 domain_id	2a6qC02
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	330 —

结构域编号 domain_id	2a6qD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1620 — YefM-like fold
同源超家族 H-superfamily homologous superfamily	10 — YefM-like domain

结构域编号 domain_id	2a6qE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	2310 — YaeB-like fold
同源超家族 H-superfamily homologous superfamily	20 — RelE-like

结构域编号 domain_id	2a6qF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	2310 — YaeB-like fold
同源超家族 H-superfamily homologous superfamily	20 — RelE-like

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7. 引用文献 (1)

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晶胞边长 a length_a	88.485 Å
晶胞边长 b length_b	88.485 Å
晶胞边长 c length_c	135.150 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	24

空间群 space_group	P 64
空间群编号 int_tables_number	172
晶系 crystal_system	—

分辨率 resolution	2.050 Å
最低分辨率 resolution_low	29.190 Å
R 因子 r_factor	0.2250
R_work r_work	0.2240
R_free r_free	0.2540

fit	/app/data/saxs_computation/a6/2a6q/2a6q.fit
pddf	/app/data/pr_computation/a6/2a6q/2a6q.pr.out
profile	/app/data/saxs_computation/a6/2a6q/2a6q.dat

Crystal structure of YefM-YoeB complex

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

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) 18 domains

SCOP 2.08 (10 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)