1iyh

Crystal structure of hematopoietic prostaglandin D synthase

Method: X-RAY DIFFRACTION D_max: 120.4 Å Quality: REASONABLE

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	1iyh
沉积日期 deposition_date	2002-08-26
结构标题 title	Crystal structure of hematopoietic prostaglandin D synthase
关键词 keywords	HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE, PGDS, GST, SIGMA-CLASS GST, LIGASE, 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	33.90 Å
回转半径 Rg (电子) rg_electron	33.56 Å
零角强度 I(0) i0	131775000.00
分子量 molecular_weight	94177.0 kDa
排除体积 excluded_volume	118820 Å³
包络体积 envelope_volume	151210 Å³
水化壳体积 shell_volume	38884 Å³
包络直径 envelope_diameter	117.8 Å
壳层 Rg shell_rg	38.78 Å
包络 Rg envelope_rg	33.13 Å
形状 Rg shape_rg	33.57 Å
总 Rg total_rg	33.95 Å
总原子数 total_atoms	6634
残基数 n_residues	792
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	120.4 Å
Rg (实空间) rg_real	34.06 Å
Rg 误差 (实空间) rg_real_error	1.28 Å
I(0) (实空间) i0_real	1.3180e+08
I(0) 误差 (实空间) i0_real_error	2.3560e+06
Rg (倒空间) rg_reciprocal	33.96 Å
I(0) (倒空间) i0_reciprocal	131800000.0000
解质量估计 total_estimate	0.7315
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	30.7 Å
偏度 Skewness skewness	0.455
峰度 Kurtosis kurtosis	-0.532
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	81960000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.612; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.668; Smooth: 0.000

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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	HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE
分子量 formula_weight	23256.7 kDa
EC 编号 ec_number	5.3.99.2
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	7616

PNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSCFPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGMSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	GLUTATHIONE
分子量 formula_weight	307.3 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	982

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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	d1iyha1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.45 — GST C-terminal domain-like
超家族 Superfamily superfamily	a.45.1 — GST C-terminal domain-like
家族 Family family	a.45.1.1 — Glutathione S-transferase (GST), C-terminal domain

结构域编号 domain_id	d1iyha2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.5 — Glutathione S-transferase (GST), N-terminal domain

结构域编号 domain_id	d1iyhb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.45 — GST C-terminal domain-like
超家族 Superfamily superfamily	a.45.1 — GST C-terminal domain-like
家族 Family family	a.45.1.1 — Glutathione S-transferase (GST), C-terminal domain

结构域编号 domain_id	d1iyhb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.5 — Glutathione S-transferase (GST), N-terminal domain

结构域编号 domain_id	d1iyhc1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.45 — GST C-terminal domain-like
超家族 Superfamily superfamily	a.45.1 — GST C-terminal domain-like
家族 Family family	a.45.1.1 — Glutathione S-transferase (GST), C-terminal domain

结构域编号 domain_id	d1iyhc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.5 — Glutathione S-transferase (GST), N-terminal domain

结构域编号 domain_id	d1iyhd1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.45 — GST C-terminal domain-like
超家族 Superfamily superfamily	a.45.1 — GST C-terminal domain-like
家族 Family family	a.45.1.1 — Glutathione S-transferase (GST), C-terminal domain

结构域编号 domain_id	d1iyhd2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.5 — Glutathione S-transferase (GST), N-terminal domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1iyhA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	1iyhA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1iyhB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	1iyhB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1iyhC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	1iyhC02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1iyhD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	1iyhD02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (1)

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晶胞边长 a length_a	49.113 Å
晶胞边长 b length_b	47.373 Å
晶胞边长 c length_c	184.696 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	97.44 °
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	1.700 Å
最低分辨率 resolution_low	30.940 Å
R 因子 r_factor	0.2050
R_work r_work	0.2050
R_free r_free	0.2380

fit	/app/data/saxs_computation/iy/1iyh/1iyh.fit
pddf	/app/data/pr_computation/iy/1iyh/1iyh.pr.out
profile	/app/data/saxs_computation/iy/1iyh/1iyh.dat