2dfu

Crystal structure of the 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Thermus Thermophilus HB8

Method: X-RAY DIFFRACTION D_max: 133.3 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	2dfu
沉积日期 deposition_date	2006-03-03
结构标题 title	Crystal structure of the 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Thermus Thermophilus HB8
关键词 keywords	;2-hydroxyhepta-2, 4-diene-1, 7-dioate isomerase, structural genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, ISOMERASE ;; ISOMERASE
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	39.17 Å
回转半径 Rg (电子) rg_electron	39.16 Å
零角强度 I(0) i0	174913000.00
分子量 molecular_weight	110280.0 kDa
排除体积 excluded_volume	139180 Å³
包络体积 envelope_volume	179490 Å³
水化壳体积 shell_volume	39716 Å³
包络直径 envelope_diameter	132.0 Å
壳层 Rg shell_rg	42.94 Å
包络 Rg envelope_rg	38.35 Å
形状 Rg shape_rg	39.17 Å
总 Rg total_rg	39.33 Å
总原子数 total_atoms	7795
残基数 n_residues	996
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	133.3 Å
Rg (实空间) rg_real	39.56 Å
Rg 误差 (实空间) rg_real_error	1.31 Å
I(0) (实空间) i0_real	1.7490e+08
I(0) 误差 (实空间) i0_real_error	3.2790e+06
Rg (倒空间) rg_reciprocal	39.33 Å
I(0) (倒空间) i0_reciprocal	174900000.0000
解质量估计 total_estimate	0.8157
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	33.3 Å
偏度 Skewness skewness	0.428
峰度 Kurtosis kurtosis	-0.676
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	23670000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.690; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.688; Smooth: 0.843

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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 (2)

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6. 折叠分类 (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

结构域编号 domain_id	2dfuA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	370 — FAH

结构域编号 domain_id	2dfuA02
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	2dfuB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	370 — FAH

结构域编号 domain_id	2dfuB02
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	2dfuC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	370 — FAH

结构域编号 domain_id	2dfuC02
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	2dfuD01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	370 — FAH

结构域编号 domain_id	2dfuD02
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	93.340 Å
晶胞边长 b length_b	73.412 Å
晶胞边长 c length_c	122.632 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	111.78 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	2.200 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.1970
R_work r_work	0.1970
R_free r_free	0.2240

描述 description	probable 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase
分子量 formula_weight	29423.4 kDa
EC 编号 ec_number	5.3.3.10
来源方法 src_method	man
拷贝数 entity_count	4

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	8438

Crystal structure of the 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Thermus Thermophilus HB8

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Thermus thermophilus
NCBI 分类编号 ncbi_taxonomy_id	300852
宿主生物 host_organism	Escherichia coli BL21(DE3)

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	643

fit	/app/data/saxs_computation/df/2dfu/2dfu.fit
pddf	/app/data/pr_computation/df/2dfu/2dfu.pr.out
profile	/app/data/saxs_computation/df/2dfu/2dfu.dat