1l2w

Crystal Structure of the Yersinia Virulence Effector YopE Chaperone-binding Domain in Complex with its Secretion Chaperone, SycE

Method: X-RAY DIFFRACTION D_max: 120.8 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	1l2w
沉积日期 deposition_date	2002-02-25
结构标题 title	Crystal Structure of the Yersinia Virulence Effector YopE Chaperone-binding Domain in Complex with its Secretion Chaperone, SycE
关键词 keywords	CHAPERONE AND VIRULENCE PROTEIN, CHAPERONE; CHAPERONE
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	38.00 Å
回转半径 Rg (电子) rg_electron	37.58 Å
零角强度 I(0) i0	263542000.00
分子量 molecular_weight	131060.0 kDa
排除体积 excluded_volume	163850 Å³
包络体积 envelope_volume	223130 Å³
水化壳体积 shell_volume	50794 Å³
包络直径 envelope_diameter	124.8 Å
壳层 Rg shell_rg	42.74 Å
包络 Rg envelope_rg	36.79 Å
形状 Rg shape_rg	37.58 Å
总 Rg total_rg	37.92 Å
总原子数 total_atoms	9232
残基数 n_residues	1172
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	120.8 Å
Rg (实空间) rg_real	37.90 Å
Rg 误差 (实空间) rg_real_error	0.93 Å
I(0) (实空间) i0_real	2.6350e+08
I(0) 误差 (实空间) i0_real_error	4.4920e+06
Rg (倒空间) rg_reciprocal	37.97 Å
I(0) (倒空间) i0_reciprocal	263600000.0000
解质量估计 total_estimate	0.8987
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	48.9 Å
偏度 Skewness skewness	0.199
峰度 Kurtosis kurtosis	-0.558
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	63280000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.836

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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	YopE regulator
分子量 formula_weight	13843.6 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	A,B,C,D,E,F,G,H
原子数 atom_count	9594

MGYSFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILMFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEMLVQGAERLQTSSL

来源 Source

来源生物 organism	Yersinia pseudotuberculosis
NCBI 分类编号 ncbi_taxonomy_id	633
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	Outer membrane virulence protein yopE
分子量 formula_weight	7278.0 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	I,J,K,L

VSGSSSVGEMSGRSVSQQTSDQYANNLAGRTESPQGSSLASRIIERLSSVAHSVIGFIQRMFSEGSHKP

来源 Source

来源生物 organism	Yersinia pseudotuberculosis
NCBI 分类编号 ncbi_taxonomy_id	633
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	362

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6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1l2wa_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.198 — Secretion chaperone-like
超家族 Superfamily superfamily	d.198.1 — Type III secretory system chaperone-like
家族 Family family	d.198.1.1 — Type III secretory system chaperone

结构域编号 domain_id	d1l2wb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.198 — Secretion chaperone-like
超家族 Superfamily superfamily	d.198.1 — Type III secretory system chaperone-like
家族 Family family	d.198.1.1 — Type III secretory system chaperone

结构域编号 domain_id	d1l2wc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.198 — Secretion chaperone-like
超家族 Superfamily superfamily	d.198.1 — Type III secretory system chaperone-like
家族 Family family	d.198.1.1 — Type III secretory system chaperone

结构域编号 domain_id	d1l2wd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.198 — Secretion chaperone-like
超家族 Superfamily superfamily	d.198.1 — Type III secretory system chaperone-like
家族 Family family	d.198.1.1 — Type III secretory system chaperone

结构域编号 domain_id	d1l2we_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.198 — Secretion chaperone-like
超家族 Superfamily superfamily	d.198.1 — Type III secretory system chaperone-like
家族 Family family	d.198.1.1 — Type III secretory system chaperone

结构域编号 domain_id	d1l2wf_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.198 — Secretion chaperone-like
超家族 Superfamily superfamily	d.198.1 — Type III secretory system chaperone-like
家族 Family family	d.198.1.1 — Type III secretory system chaperone

结构域编号 domain_id	d1l2wg_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.198 — Secretion chaperone-like
超家族 Superfamily superfamily	d.198.1 — Type III secretory system chaperone-like
家族 Family family	d.198.1.1 — Type III secretory system chaperone

结构域编号 domain_id	d1l2wh_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.198 — Secretion chaperone-like
超家族 Superfamily superfamily	d.198.1 — Type III secretory system chaperone-like
家族 Family family	d.198.1.1 — Type III secretory system chaperone

结构域编号 domain_id	d1l2wi_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.184 — Non-globular alpha+beta subunits of globular proteins
超家族 Superfamily superfamily	d.184.1 — Non-globular alpha+beta subunits of globular proteins
家族 Family family	d.184.1.2 — Type III secretory system effector

结构域编号 domain_id	d1l2wj_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.184 — Non-globular alpha+beta subunits of globular proteins
超家族 Superfamily superfamily	d.184.1 — Non-globular alpha+beta subunits of globular proteins
家族 Family family	d.184.1.2 — Type III secretory system effector

结构域编号 domain_id	d1l2wk_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.184 — Non-globular alpha+beta subunits of globular proteins
超家族 Superfamily superfamily	d.184.1 — Non-globular alpha+beta subunits of globular proteins
家族 Family family	d.184.1.2 — Type III secretory system effector

结构域编号 domain_id	d1l2wl_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.184 — Non-globular alpha+beta subunits of globular proteins
超家族 Superfamily superfamily	d.184.1 — Non-globular alpha+beta subunits of globular proteins
家族 Family family	d.184.1.2 — Type III secretory system effector

CATH v4.4 (8 domains)

结构域编号 domain_id	1l2wA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1460 — Yope Regulator; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1l2wB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1460 — Yope Regulator; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1l2wC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1460 — Yope Regulator; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1l2wD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1460 — Yope Regulator; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1l2wE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1460 — Yope Regulator; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1l2wF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1460 — Yope Regulator; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1l2wG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1460 — Yope Regulator; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1l2wH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1460 — Yope Regulator; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (1)

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晶胞边长 a length_a	72.845 Å
晶胞边长 b length_b	73.352 Å
晶胞边长 c length_c	74.263 Å
晶胞夹角 α angle_alpha	103.37 °
晶胞夹角 β angle_beta	109.18 °
晶胞夹角 γ angle_gamma	107.36 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.2510
R_free r_free	0.2750

fit	/app/data/saxs_computation/l2/1l2w/1l2w.fit
pddf	/app/data/pr_computation/l2/1l2w/1l2w.pr.out
profile	/app/data/saxs_computation/l2/1l2w/1l2w.dat

Crystal Structure of the Yersinia Virulence Effector YopE Chaperone-binding Domain in Complex with its Secretion Chaperone, SycE

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) 20 domains

SCOP 2.08 (12 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)