1pyp

X-RAY DIFFRACTION STUDY OF INORGANIC PYROPHOSPHATASE FROM BAKER,S YEAST AT THE 3 ANGSTROMS RESOLUTION (RUSSIAN)

Method: X-RAY DIFFRACTION D_max: 94.6 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	1pyp
沉积日期 deposition_date	1983-02-03
结构标题 title	X-RAY DIFFRACTION STUDY OF INORGANIC PYROPHOSPHATASE FROM BAKER,S YEAST AT THE 3 ANGSTROMS RESOLUTION (RUSSIAN)
关键词 keywords	ACID ANHYDRIDE HYDROLASE; ACID ANHYDRIDE 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	27.72 Å
回转半径 Rg (电子) rg_electron	26.93 Å
零角强度 I(0) i0	61909400.00
分子量 molecular_weight	63172.0 kDa
排除体积 excluded_volume	79724 Å³
包络体积 envelope_volume	95647 Å³
水化壳体积 shell_volume	30200 Å³
包络直径 envelope_diameter	101.1 Å
壳层 Rg shell_rg	33.69 Å
包络 Rg envelope_rg	26.97 Å
形状 Rg shape_rg	26.90 Å
总 Rg total_rg	27.74 Å
总原子数 total_atoms	4472
残基数 n_residues	562
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	94.6 Å
Rg (实空间) rg_real	27.82 Å
Rg 误差 (实空间) rg_real_error	0.65 Å
I(0) (实空间) i0_real	6.1910e+07
I(0) 误差 (实空间) i0_real_error	9.1320e+05
Rg (倒空间) rg_reciprocal	27.79 Å
I(0) (倒空间) i0_reciprocal	61910000.0000
解质量估计 total_estimate	0.8615
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	29.9 Å
偏度 Skewness skewness	0.446
峰度 Kurtosis kurtosis	-0.362
角度范围 angular_range	— – 0.2850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	14580000.0000
实空间数据点数 n_real_points	58
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.771; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.936; Smooth: 0.948

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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) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1pypa_
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	d1pypb_
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	1pypA00
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	1pypB00
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 (9)

X-Ray Diffraction Study of Inorganic Pyrophosphatase from Baker,S Yeast at the 3 Angstroms Resolution (Russian)

Dokl.Akad.Nauk Sssr (1981)

PMID: -1 PRIMARY

X-Ray Structural Investigation of Inorganic Pyrophosphatase from Baker,S Yeast at 3 Angstroms Resolution

Dokl.Biochem.(Engl.Transl.) (1981)

;X-Ray Structural Investigation of Inorganic Pyrophosphatase of Baker Yeast. II. Phase Calculation and Structure Model at 6 Angstroms Resolution (Russian) ;

Kristallografiya (1980)

;X-Ray Structural Investigation of Inorganic Pyrophosphatase of Yeasts. II. Calculation of Phases and Structural Model at 6 Angstroms Resolution ;

Sov.Phys.Crystallogr.(Engl.Transl.) (1980)

;X-Ray Structural Investigation of Inorganic Pyrophosphatase of Baker Yeast. I. Growing of Crystals, Production of Derivatives and Determination of the Heavy Atom Positions in Them (Russian) ;

Kristallografiya (1980)

;X-Ray Structural Investigation of Inorganic-Pyrophosphatase of Yeasts. I. Growth of Crystals, Formation of Derivatives, and Determination of the Positions of Their Heavy Atoms ;

Sov.Phys.Crystallogr.(Engl.Transl.) (1980)

X-Ray Diffraction Study of Inorganic Pyrophosphatase from Baker,S Yeast at the 6 Angstroms Resolution (Russian)

Dokl.Akad.Nauk Sssr (1978)

X-Ray Diffraction Study of Inorganic Pyrophosphatase from Baker,S Yeast at a Resolution of 6 Angstroms

Dokl.Biochem.(Engl.Transl.) (1978)

Covalent Structural Analysis of Yeast Inorganic Pyrophosphatase

J.Biol.Chem. (1978)

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晶胞边长 a length_a	52.230 Å
晶胞边长 b length_b	70.290 Å
晶胞边长 c length_c	95.470 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	99.59 °
晶胞分子数 Z z_pdb	4

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

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

描述 description	INORGANIC PYROPHOSPHATASE
分子量 formula_weight	32079.2 kDa
EC 编号 ec_number	3.6.1.1
来源方法 src_method	man
拷贝数 entity_count	2

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	4472

X-RAY DIFFRACTION STUDY OF INORGANIC PYROPHOSPHATASE FROM BAKER,S YEAST AT THE 3 ANGSTROMS RESOLUTION (RUSSIAN)

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

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. 引用文献 (9)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932

fit	/app/data/saxs_computation/py/1pyp/1pyp.fit
pddf	/app/data/pr_computation/py/1pyp/1pyp.pr.out
profile	/app/data/saxs_computation/py/1pyp/1pyp.dat