1hpu

;5'-NUCLEOTIDASE (CLOSED FORM), COMPLEX WITH AMPCP ;

Method: X-RAY DIFFRACTION D_max: 156.8 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	1hpu
沉积日期 deposition_date	2000-12-13
结构标题 title	;5'-NUCLEOTIDASE (CLOSED FORM), COMPLEX WITH AMPCP ;
关键词 keywords	metalloenzyme, metallophosphatase, domain rotation, 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	47.48 Å
回转半径 Rg (电子) rg_electron	47.27 Å
零角强度 I(0) i0	828108000.00
分子量 molecular_weight	234920.0 kDa
排除体积 excluded_volume	292390 Å³
包络体积 envelope_volume	393210 Å³
水化壳体积 shell_volume	70568 Å³
包络直径 envelope_diameter	163.7 Å
壳层 Rg shell_rg	50.22 Å
包络 Rg envelope_rg	46.36 Å
形状 Rg shape_rg	47.26 Å
总 Rg total_rg	47.41 Å
总原子数 total_atoms	16516
残基数 n_residues	2100
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	156.8 Å
Rg (实空间) rg_real	47.35 Å
Rg 误差 (实空间) rg_real_error	1.27 Å
I(0) (实空间) i0_real	8.2810e+08
I(0) 误差 (实空间) i0_real_error	1.5070e+07
Rg (倒空间) rg_reciprocal	47.48 Å
I(0) (倒空间) i0_reciprocal	828200000.0000
解质量估计 total_estimate	0.8854
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	66.5 Å
偏度 Skewness skewness	0.154
峰度 Kurtosis kurtosis	-0.508
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	59040000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.866

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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 (4)

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	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	17735

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	8

Entity 3 non-polymer

描述 description	PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
分子量 formula_weight	425.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 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	1219

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1hpua1
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	d1hpua2
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	d1hpub1
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	d1hpub2
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	d1hpuc1
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	d1hpuc2
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	d1hpud1
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	d1hpud2
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 (8 domains)

结构域编号 domain_id	1hpuA01
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	1hpuA02
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	1hpuB01
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	1hpuB02
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	1hpuC01
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	1hpuC02
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	1hpuD01
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	1hpuD02
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	89.400 Å
晶胞边长 b length_b	89.960 Å
晶胞边长 c length_c	96.260 Å
晶胞夹角 α angle_alpha	110.79 °
晶胞夹角 β angle_beta	106.43 °
晶胞夹角 γ angle_gamma	107.76 °
晶胞分子数 Z z_pdb	4

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

分辨率 resolution	1.850 Å
最低分辨率 resolution_low	28.590 Å
R 因子 r_factor	0.2070
R_work r_work	0.2070
R_free r_free	0.2340

fit	/app/data/saxs_computation/hp/1hpu/1hpu.fit
pddf	/app/data/pr_computation/hp/1hpu/1hpu.pr.out
profile	/app/data/saxs_computation/hp/1hpu/1hpu.dat