SAXSdb — 1ypp

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ypp
沉积日期 deposition_date	1996-05-29
结构标题 title	ACID ANHYDRIDE HYDROLASE
关键词 keywords	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	27.50 Å
回转半径 Rg (电子) rg_electron	26.86 Å
零角强度 I(0) i0	65937400.00
分子量 molecular_weight	64329.0 kDa
排除体积 excluded_volume	80669 Å³
包络体积 envelope_volume	95341 Å³
水化壳体积 shell_volume	30241 Å³
包络直径 envelope_diameter	96.8 Å
壳层 Rg shell_rg	33.65 Å
包络 Rg envelope_rg	26.81 Å
形状 Rg shape_rg	26.86 Å
总 Rg total_rg	27.58 Å
总原子数 total_atoms	4524
残基数 n_residues	564
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	90.8 Å
Rg (实空间) rg_real	27.62 Å
Rg 误差 (实空间) rg_real_error	0.75 Å
I(0) (实空间) i0_real	6.5940e+07
I(0) 误差 (实空间) i0_real_error	1.0300e+06
Rg (倒空间) rg_reciprocal	27.58 Å
I(0) (倒空间) i0_reciprocal	65940000.0000
解质量估计 total_estimate	0.8765
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	28.2 Å
偏度 Skewness skewness	0.440
峰度 Kurtosis kurtosis	-0.404
角度范围 angular_range	— – 0.2900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	19930000.0000
实空间数据点数 n_real_points	59
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.827; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.957

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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	INORGANIC PYROPHOSPHATASE
分子量 formula_weight	32151.2 kDa
EC 编号 ec_number	3.6.1.1
来源方法 src_method	nat
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	4746

TYTTRQIGAKNTLEYKVYIEKDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTAKGKLRFVRNCFPHHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMALLDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPENQFAFSGEAKNKKYALDIIKETHDSWKQLIAGKSSDSKGIDLTNVTLPDTPTYSKAASDAIPPASPKADAPIDKSIDKWFFISGSV

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	PHOSPHATE ION
分子量 formula_weight	95.0 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	222

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6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1yppa_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.5 — Inorganic pyrophosphatase
家族 Family family	b.40.5.1 — Inorganic pyrophosphatase

结构域编号 domain_id	d1yppb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.5 — Inorganic pyrophosphatase
家族 Family family	b.40.5.1 — Inorganic pyrophosphatase

CATH v4.4 (2 domains)

结构域编号 domain_id	1yppA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	80 — Inorganic Pyrophosphatase
同源超家族 H-superfamily homologous superfamily	10 — Inorganic pyrophosphatase

结构域编号 domain_id	1yppB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	80 — Inorganic Pyrophosphatase
同源超家族 H-superfamily homologous superfamily	10 — Inorganic pyrophosphatase

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7. 引用文献 (13)

X-ray structure of yeast inorganic pyrophosphatase complexed with manganese and phosphate.

Eur.J.Biochem. (1996)

PMID: 8706712 · DOI: 10.1111/j.1432-1033.1996.0220u.x PRIMARY

Structure of Inorganic Pyrophosphatase from E. Coli and its Complex with a Mn2+ Ion at 2.2 Angstroms Resolution

Crystallography reports (1996)

New Crystal Forms of Escherichia Coli and Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatases

Acta Crystallogr.,Sect.D (1995)

Crystal Structure of Inorganic Pyrophosphatase from Thermus Thermophilus

Protein Sci. (1994)

The Structure of E.Coli Soluble Inorganic Pyrophosphatase at 2.7 A Resolution

Protein Eng. (1994)

Two Pathways of Pyrophosphate Hydrolysis and Synthesis by Yeast Inorganic Pyrophosphatase

Eur.J.Biochem. (1992)

Crystal Structure of Mnpi Complex of Yeast Inorganic Pyrophosphatase at 2.35 Angstroms Resolution (Russian)

Kristallografiya (1991)

The Growing of Crystals of Inorganic Pyrophosphatase from Yeast with Metal Ions and Phosphate (Russian)

Kristallografiya (1990)

A Conformational Hypothesis of the Trans-Ligation of Metals which Activate Pyrophosphatase and Related Enzymes (Russian)

Bioorg.Khim. (1986)

Investigations of the Metal Ion-Binding Sites of Yeast Inorganic Pyrophosphatase

J.Biol.Chem. (1984)

Inorganic Pyrophosphatase from Yeast at 3 A Resolution (Russian)

Bioorg.Khim. (1984)

The Mechanism of Action of Yeast Inorganic Pyrophosphatase

Methods Enzymol. (1982)

Yeast Inorganic Pyrophosphatase: Studies on Metal Binding

Eur.J.Biochem. (1974)

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晶胞边长 a length_a	116.000 Å
晶胞边长 b length_b	106.200 Å
晶胞边长 c length_c	56.100 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	2.400 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/yp/1ypp/1ypp.fit
pddf	/app/data/pr_computation/yp/1ypp/1ypp.pr.out
profile	/app/data/saxs_computation/yp/1ypp/1ypp.dat

ACID ANHYDRIDE HYDROLASE

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution