1r56

UNCOMPLEXED URATE OXIDASE FROM ASPERGILLUS FLAVUS

Method: X-RAY DIFFRACTION D_max: 165.8 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	1r56
沉积日期 deposition_date	2003-10-09
结构标题 title	UNCOMPLEXED URATE OXIDASE FROM ASPERGILLUS FLAVUS
关键词 keywords	OXIDOREDUCTASE, URIC ACID DEGRADATION, DIMERIC BARREL, TUNNEL-SHAPED PROTEIN; OXIDOREDUCTASE
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	49.49 Å
回转半径 Rg (电子) rg_electron	49.65 Å
零角强度 I(0) i0	1043690000.00
分子量 molecular_weight	267960.0 kDa
排除体积 excluded_volume	334900 Å³
包络体积 envelope_volume	459610 Å³
水化壳体积 shell_volume	77231 Å³
包络直径 envelope_diameter	165.8 Å
壳层 Rg shell_rg	52.84 Å
包络 Rg envelope_rg	48.62 Å
形状 Rg shape_rg	49.66 Å
总 Rg total_rg	49.75 Å
总原子数 total_atoms	18906
残基数 n_residues	2357
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	165.8 Å
Rg (实空间) rg_real	49.77 Å
Rg 误差 (实空间) rg_real_error	1.52 Å
I(0) (实空间) i0_real	1.0440e+09
I(0) 误差 (实空间) i0_real_error	2.1020e+07
Rg (倒空间) rg_reciprocal	49.49 Å
I(0) (倒空间) i0_reciprocal	1043000000.0000
解质量估计 total_estimate	0.7660
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	46.6 Å
偏度 Skewness skewness	0.406
峰度 Kurtosis kurtosis	-0.642
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	1284000000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.661; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; 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 (3)

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

结构域编号 domain_id	d1r56a1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.96 — T-fold
超家族 Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
家族 Family family	d.96.1.4 — Urate oxidase (uricase)

结构域编号 domain_id	d1r56a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.96 — T-fold
超家族 Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
家族 Family family	d.96.1.4 — Urate oxidase (uricase)

结构域编号 domain_id	d1r56b1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.96 — T-fold
超家族 Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
家族 Family family	d.96.1.4 — Urate oxidase (uricase)

结构域编号 domain_id	d1r56b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.96 — T-fold
超家族 Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
家族 Family family	d.96.1.4 — Urate oxidase (uricase)

结构域编号 domain_id	d1r56c1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.96 — T-fold
超家族 Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
家族 Family family	d.96.1.4 — Urate oxidase (uricase)

结构域编号 domain_id	d1r56c2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.96 — T-fold
超家族 Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
家族 Family family	d.96.1.4 — Urate oxidase (uricase)

结构域编号 domain_id	d1r56d1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.96 — T-fold
超家族 Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
家族 Family family	d.96.1.4 — Urate oxidase (uricase)

结构域编号 domain_id	d1r56d2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.96 — T-fold
超家族 Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
家族 Family family	d.96.1.4 — Urate oxidase (uricase)

结构域编号 domain_id	d1r56e1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.96 — T-fold
超家族 Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
家族 Family family	d.96.1.4 — Urate oxidase (uricase)

结构域编号 domain_id	d1r56e2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.96 — T-fold
超家族 Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
家族 Family family	d.96.1.4 — Urate oxidase (uricase)

结构域编号 domain_id	d1r56f1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.96 — T-fold
超家族 Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
家族 Family family	d.96.1.4 — Urate oxidase (uricase)

结构域编号 domain_id	d1r56f2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.96 — T-fold
超家族 Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
家族 Family family	d.96.1.4 — Urate oxidase (uricase)

结构域编号 domain_id	d1r56g1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.96 — T-fold
超家族 Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
家族 Family family	d.96.1.4 — Urate oxidase (uricase)

结构域编号 domain_id	d1r56g2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.96 — T-fold
超家族 Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
家族 Family family	d.96.1.4 — Urate oxidase (uricase)

结构域编号 domain_id	d1r56h1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.96 — T-fold
超家族 Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
家族 Family family	d.96.1.4 — Urate oxidase (uricase)

结构域编号 domain_id	d1r56h2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.96 — T-fold
超家族 Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
家族 Family family	d.96.1.4 — Urate oxidase (uricase)

CATH v4.4 (8 domains)

结构域编号 domain_id	1r56A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	270 — Urate Oxidase
同源超家族 H-superfamily homologous superfamily	10 — Urate Oxidase;

结构域编号 domain_id	1r56B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	270 — Urate Oxidase
同源超家族 H-superfamily homologous superfamily	10 — Urate Oxidase;

结构域编号 domain_id	1r56C00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	270 — Urate Oxidase
同源超家族 H-superfamily homologous superfamily	10 — Urate Oxidase;

结构域编号 domain_id	1r56D00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	270 — Urate Oxidase
同源超家族 H-superfamily homologous superfamily	10 — Urate Oxidase;

结构域编号 domain_id	1r56E00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	270 — Urate Oxidase
同源超家族 H-superfamily homologous superfamily	10 — Urate Oxidase;

结构域编号 domain_id	1r56F00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	270 — Urate Oxidase
同源超家族 H-superfamily homologous superfamily	10 — Urate Oxidase;

结构域编号 domain_id	1r56G00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	270 — Urate Oxidase
同源超家族 H-superfamily homologous superfamily	10 — Urate Oxidase;

结构域编号 domain_id	1r56H00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	270 — Urate Oxidase
同源超家族 H-superfamily homologous superfamily	10 — Urate Oxidase;

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7. 引用文献 (2)

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晶胞边长 a length_a	82.590 Å
晶胞边长 b length_b	141.843 Å
晶胞边长 c length_c	134.959 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	92.69 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

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	2.300 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	—
R_work r_work	0.1620
R_free r_free	0.2140

描述 description	Uricase
分子量 formula_weight	34199.6 kDa
EC 编号 ec_number	1.7.3.3
来源方法 src_method	nat
拷贝数 entity_count	8

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H
原子数 atom_count	19240

UNCOMPLEXED URATE OXIDASE FROM ASPERGILLUS FLAVUS

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

Entity 2 non-polymer

Entity 3 water

6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

CATH v4.4 (8 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)

描述 description	DI(HYDROXYETHYL)ETHER
分子量 formula_weight	106.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	334

fit	/app/data/saxs_computation/r5/1r56/1r56.fit
pddf	/app/data/pr_computation/r5/1r56/1r56.pr.out
profile	/app/data/saxs_computation/r5/1r56/1r56.dat