SAXSdb — 1ho5

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ho5
沉积日期 deposition_date	2000-12-08
结构标题 title	;5'-NUCLEOTIDASE (E. COLI) IN COMPLEX WITH ADENOSINE AND PHOSPHATE ;
关键词 keywords	metalloprotein, domain movement, HYDROLASE; HYDROLASE
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	38.35 Å
回转半径 Rg (电子) rg_electron	38.80 Å
零角强度 I(0) i0	214745000.00
分子量 molecular_weight	117340.0 kDa
排除体积 excluded_volume	146090 Å³
包络体积 envelope_volume	187260 Å³
水化壳体积 shell_volume	42632 Å³
包络直径 envelope_diameter	147.2 Å
壳层 Rg shell_rg	41.39 Å
包络 Rg envelope_rg	38.68 Å
形状 Rg shape_rg	38.78 Å
总 Rg total_rg	39.01 Å
总原子数 total_atoms	8252
残基数 n_residues	1050
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	138.1 Å
Rg (实空间) rg_real	38.85 Å
Rg 误差 (实空间) rg_real_error	1.75 Å
I(0) (实空间) i0_real	2.1470e+08
I(0) 误差 (实空间) i0_real_error	4.5120e+06
Rg (倒空间) rg_reciprocal	38.55 Å
I(0) (倒空间) i0_reciprocal	214700000.0000
解质量估计 total_estimate	0.7905
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	33.7 Å
偏度 Skewness skewness	0.575
峰度 Kurtosis kurtosis	-0.311
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	49380000.0000
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: 0.595; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.646; Smooth: 0.841

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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 (5)

Entity 1 polymer

描述 description	5'-NUCLEOTIDASE
分子量 formula_weight	58277.6 kDa
EC 编号 ec_number	3.1.3.5, 3.6.1.45
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,B
原子数 atom_count	8607

YEQDKTYKITVLHTNDHHGHFWRNEYGEYGLAAQKTLVDGIRKEVAAEGGSVLLLSGGDINTGVPESDLQDAEPDFRGMNLVGYDAMAIGNHEFDNPLTVLRQQEKWAKFPLLSANIYQKSTGERLFKPWALFKRQDLKIAVIGLTTDDTAKIGNPEYFTDIEFRKPADEAKLVIQELQQTEKPDIIIAATHMGHYDNGEHGSNAPGDVEMARALPAGSLAMIVGGHSQDPVCMAAENKKQVDYVPGTPCKPDQQNGIWIVQAHEWGKYVGRADFEFRNGEMKMVNYQLIPVNLKKKVTWEDGKSERVLYTPEIAENQQMISLLSPFQNKGKAQLEVKIGETNGRLEGDRDKVRFVQTNMGRLILAAQMDRTGADFAVMSGGGIRDSIEAGDISYKNVLKVQPFGNVVVYADMTGKEVIDYLTAVAQMKPDSGAYPQFANVSFVAKDGKLNDLKIKGEPVDPAKTYRMATLNFNATGGDGYPRLDNKPGYVNTGFIDAEVLKAYIQKSSPLDVSVYEPKGEVSWQ

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

Entity 2 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	ADENOSINE
分子量 formula_weight	267.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 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	355

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1ho5a1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.114 — 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain
超家族 Superfamily superfamily	d.114.1 — 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain
家族 Family family	d.114.1.1 — 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain

结构域编号 domain_id	d1ho5a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.159 — Metallo-dependent phosphatases
超家族 Superfamily superfamily	d.159.1 — Metallo-dependent phosphatases
家族 Family family	d.159.1.2 — 5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain

结构域编号 domain_id	d1ho5b1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.114 — 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain
超家族 Superfamily superfamily	d.114.1 — 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain
家族 Family family	d.114.1.1 — 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain

结构域编号 domain_id	d1ho5b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.159 — Metallo-dependent phosphatases
超家族 Superfamily superfamily	d.159.1 — Metallo-dependent phosphatases
家族 Family family	d.159.1.2 — 5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1ho5A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Metallo-dependent phosphatases

结构域编号 domain_id	1ho5A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	780 — 5'-nucleotidase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — 5'-Nucleotidase, C-terminal domain

结构域编号 domain_id	1ho5B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Metallo-dependent phosphatases

结构域编号 domain_id	1ho5B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	780 — 5'-nucleotidase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — 5'-Nucleotidase, C-terminal domain

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7. 引用文献 (3)

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晶胞边长 a length_a	69.900 Å
晶胞边长 b length_b	75.700 Å
晶胞边长 c length_c	221.700 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	8

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	2.100 Å
最低分辨率 resolution_low	29.560 Å
R 因子 r_factor	0.2380
R_work r_work	0.2380
R_free r_free	0.2790

fit	/app/data/saxs_computation/ho/1ho5/1ho5.fit
pddf	/app/data/pr_computation/ho/1ho5/1ho5.pr.out
profile	/app/data/saxs_computation/ho/1ho5/1ho5.dat

;5'-NUCLEOTIDASE (E. COLI) IN COMPLEX WITH ADENOSINE AND PHOSPHATE ;

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