1oey

Heterodimer of p40phox and p67phox PB1 domains from human NADPH oxidase

Method: X-RAY DIFFRACTION D_max: 129.6 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	1oey
沉积日期 deposition_date	2003-04-02
结构标题 title	Heterodimer of p40phox and p67phox PB1 domains from human NADPH oxidase
关键词 keywords	IMMUNE SYSTEM, PB1 HETERODIMER-COMPLEX, NADPH OXIDASE, PB1 DOMAIN, HETERODIMERIZATION; IMMUNE SYSTEM
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	38.17 Å
回转半径 Rg (电子) rg_electron	37.86 Å
零角强度 I(0) i0	120626000.00
分子量 molecular_weight	86990.0 kDa
排除体积 excluded_volume	108070 Å³
包络体积 envelope_volume	156970 Å³
水化壳体积 shell_volume	36850 Å³
包络直径 envelope_diameter	138.0 Å
壳层 Rg shell_rg	40.82 Å
包络 Rg envelope_rg	37.36 Å
形状 Rg shape_rg	37.82 Å
总 Rg total_rg	38.18 Å
总原子数 total_atoms	6032
残基数 n_residues	696
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	129.6 Å
Rg (实空间) rg_real	38.28 Å
Rg 误差 (实空间) rg_real_error	1.44 Å
I(0) (实空间) i0_real	1.2060e+08
I(0) 误差 (实空间) i0_real_error	2.1450e+06
Rg (倒空间) rg_reciprocal	38.21 Å
I(0) (倒空间) i0_reciprocal	120600000.0000
解质量估计 total_estimate	0.8579
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	50.6 Å
偏度 Skewness skewness	0.296
峰度 Kurtosis kurtosis	-0.397
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	7925000.0000
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: 0.851; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; Smooth: 0.671

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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 (3)

Entity 1 polymer

描述 description	NEUTROPHIL CYTOSOL FACTOR 2
分子量 formula_weight	9940.8 kDa
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	6382

GSHMAYTLKVHYKYTVVMKTQPGLPYSQVRDMVSKKLELRLEHTKLSYRPRDSNELVPLSEDSMKDAWGQVKNYCLTLWCENT

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 BL21(DE3)

Entity 2 polymer

描述 description	NEUTROPHIL CYTOSOL FACTOR 4
分子量 formula_weight	12848.1 kDa
突变 mutation	YES
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	J,K,L,M

GSHMTNWLRVYYYEDTISTIKDIAVEEDLSSTPLLKDLLELTRREFQREDIALNYRDAEGDLVRLLSDEDVALMVRQARGLPSQKRLFPWKLHITQKDNYRVYNTMP

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 BL21(DE3)

Entity 3 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	343

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6. 折叠分类 (SCOP + CATH) 19 domains

SCOP 2.08 (11 domains)

结构域编号 domain_id	d1oeya1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.2 — CAD & PB1 domains
家族 Family family	d.15.2.2 — PB1 domain

结构域编号 domain_id	d1oeya2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1oeyb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.2 — CAD & PB1 domains
家族 Family family	d.15.2.2 — PB1 domain

结构域编号 domain_id	d1oeyb2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1oeyc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.2 — CAD & PB1 domains
家族 Family family	d.15.2.2 — PB1 domain

结构域编号 domain_id	d1oeyd1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.2 — CAD & PB1 domains
家族 Family family	d.15.2.2 — PB1 domain

结构域编号 domain_id	d1oeyd2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1oeyj_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.2 — CAD & PB1 domains
家族 Family family	d.15.2.2 — PB1 domain

结构域编号 domain_id	d1oeyk_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.2 — CAD & PB1 domains
家族 Family family	d.15.2.2 — PB1 domain

结构域编号 domain_id	d1oeyl_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.2 — CAD & PB1 domains
家族 Family family	d.15.2.2 — PB1 domain

结构域编号 domain_id	d1oeym_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.2 — CAD & PB1 domains
家族 Family family	d.15.2.2 — PB1 domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1oeyA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

结构域编号 domain_id	1oeyB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

结构域编号 domain_id	1oeyC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

结构域编号 domain_id	1oeyD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

结构域编号 domain_id	1oeyJ00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

结构域编号 domain_id	1oeyK00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

结构域编号 domain_id	1oeyL00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

结构域编号 domain_id	1oeyM00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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7. 引用文献 (1)

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晶胞边长 a length_a	151.422 Å
晶胞边长 b length_b	151.422 Å
晶胞边长 c length_c	68.317 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	120.00 °
晶胞分子数 Z z_pdb	24

空间群 space_group	P 64
空间群编号 int_tables_number	172
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	100.000 Å
R 因子 r_factor	0.2120
R_work r_work	0.2100
R_free r_free	0.2520

fit	/app/data/saxs_computation/oe/1oey/1oey.fit
pddf	/app/data/pr_computation/oe/1oey/1oey.pr.out
profile	/app/data/saxs_computation/oe/1oey/1oey.dat

Heterodimer of p40phox and p67phox PB1 domains from human NADPH oxidase

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

5. 实体与聚合体信息 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 water

6. 折叠分类 (SCOP + CATH) 19 domains

SCOP 2.08 (11 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)