SAXSdb — 1sv6

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1sv6
沉积日期 deposition_date	2004-03-28
结构标题 title	Crystal structure of 2-hydroxypentadienoic acid hydratase from Escherichia Coli
关键词 keywords	;Hydratase, Structural genomics, NYSGXRC target T795, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, lyase ;; LYASE
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	36.81 Å
回转半径 Rg (电子) rg_electron	36.00 Å
零角强度 I(0) i0	313220000.00
分子量 molecular_weight	140760.0 kDa
排除体积 excluded_volume	175010 Å³
包络体积 envelope_volume	217550 Å³
水化壳体积 shell_volume	48292 Å³
包络直径 envelope_diameter	113.4 Å
壳层 Rg shell_rg	44.00 Å
包络 Rg envelope_rg	35.97 Å
形状 Rg shape_rg	36.00 Å
总 Rg total_rg	36.50 Å
总原子数 total_atoms	9890
残基数 n_residues	1305
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	112.7 Å
Rg (实空间) rg_real	36.69 Å
Rg 误差 (实空间) rg_real_error	0.70 Å
I(0) (实空间) i0_real	3.1320e+08
I(0) 误差 (实空间) i0_real_error	4.9040e+06
Rg (倒空间) rg_reciprocal	36.77 Å
I(0) (倒空间) i0_reciprocal	313200000.0000
解质量估计 total_estimate	0.8845
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	49.8 Å
偏度 Skewness skewness	0.170
峰度 Kurtosis kurtosis	-0.604
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	118700000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.972; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.577

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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 (1)

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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	d1sv6a_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.177 — FAH
超家族 Superfamily superfamily	d.177.1 — FAH
家族 Family family	d.177.1.1 — FAH

结构域编号 domain_id	d1sv6b_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.177 — FAH
超家族 Superfamily superfamily	d.177.1 — FAH
家族 Family family	d.177.1.1 — FAH

结构域编号 domain_id	d1sv6c_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.177 — FAH
超家族 Superfamily superfamily	d.177.1 — FAH
家族 Family family	d.177.1.1 — FAH

结构域编号 domain_id	d1sv6d_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.177 — FAH
超家族 Superfamily superfamily	d.177.1 — FAH
家族 Family family	d.177.1.1 — FAH

结构域编号 domain_id	d1sv6e_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.177 — FAH
超家族 Superfamily superfamily	d.177.1 — FAH
家族 Family family	d.177.1.1 — FAH

CATH v4.4 (5 domains)

结构域编号 domain_id	1sv6A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	850 — Fumarylacetoacetate hydrolase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Fumarylacetoacetase-like, C-terminal domain

结构域编号 domain_id	1sv6B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	850 — Fumarylacetoacetate hydrolase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Fumarylacetoacetase-like, C-terminal domain

结构域编号 domain_id	1sv6C00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	850 — Fumarylacetoacetate hydrolase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Fumarylacetoacetase-like, C-terminal domain

结构域编号 domain_id	1sv6D00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	850 — Fumarylacetoacetate hydrolase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Fumarylacetoacetase-like, C-terminal domain

结构域编号 domain_id	1sv6E00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	850 — Fumarylacetoacetate hydrolase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Fumarylacetoacetase-like, C-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	55.222 Å
晶胞边长 b length_b	121.507 Å
晶胞边长 c length_c	111.796 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	94.10 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	10

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2430
R_work r_work	0.2390
R_free r_free	0.2670

描述 description	2-keto-4-pentenoate hydratase
分子量 formula_weight	28919.8 kDa
EC 编号 ec_number	4.2.1.-
来源方法 src_method	man
拷贝数 entity_count	5

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E
原子数 atom_count	9890

Crystal structure of 2-hydroxypentadienoic acid hydratase from Escherichia Coli

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 (1)

Entity 1 polymer

聚合体 Polymer

来源 Source

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)

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/sv/1sv6/1sv6.fit
pddf	/app/data/pr_computation/sv/1sv6/1sv6.pr.out
profile	/app/data/saxs_computation/sv/1sv6/1sv6.dat