SAXSdb — 1j2g

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1j2g
沉积日期 deposition_date	2003-01-05
结构标题 title	Crystal structure of Urate oxidase from Bacillus SP. TB-90 co-crystallized with 8-Azaxanthine
关键词 keywords	T-fold barrel, purine, OXIDOREDUCTASE; 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	32.40 Å
回转半径 Rg (电子) rg_electron	30.84 Å
零角强度 I(0) i0	302689000.00
分子量 molecular_weight	140770.0 kDa
排除体积 excluded_volume	176870 Å³
包络体积 envelope_volume	220300 Å³
水化壳体积 shell_volume	55774 Å³
包络直径 envelope_diameter	96.3 Å
壳层 Rg shell_rg	40.65 Å
包络 Rg envelope_rg	30.32 Å
形状 Rg shape_rg	30.81 Å
总 Rg total_rg	31.80 Å
总原子数 total_atoms	9956
残基数 n_residues	1224
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	89.9 Å
Rg (实空间) rg_real	32.04 Å
Rg 误差 (实空间) rg_real_error	0.27 Å
I(0) (实空间) i0_real	3.0270e+08
I(0) 误差 (实空间) i0_real_error	3.6340e+06
Rg (倒空间) rg_reciprocal	32.19 Å
I(0) (倒空间) i0_reciprocal	302700000.0000
解质量估计 total_estimate	0.9040
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	44.0 Å
偏度 Skewness skewness	-0.074
峰度 Kurtosis kurtosis	-0.556
角度范围 angular_range	— – 0.2450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	162900000.0000
实空间数据点数 n_real_points	50
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.958; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.911

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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	Uricase
分子量 formula_weight	36581.2 kDa
EC 编号 ec_number	1.7.3.3
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	10365

MTKHKERVMYYGKGDVFAYRTYLKPLTGVRTIPESPFSGRDHILFGVNVKISVGGTKLLTSFTKGDNSLVVATDSMKNFIQKHLASYTGTTIEGFLEYVATSFLKKYSHIEKISLIGEEIPFETTFAVKNGNRAASELVFKKSRNEYATAYLNMVRNEDNTLNITEQQSGLAGLQLIKVSGNSFVGFIRDEYTTLPEDSNRPLFVYLNIKWKYKNTEDSFGTNPENYVAAEQIRDIATSVFHETETLSIQHLIYLIGRRILERFPQLQEVYFESQNHTWDKIVEEIPESEGKVYTEPRPPYGFQCFTVTQEDLPHENIL

来源 Source

来源生物 organism	Bacillus sp.
NCBI 分类编号 ncbi_taxonomy_id	36824
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	8-AZAXANTHINE
分子量 formula_weight	153.1 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	409

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1j2ga1
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	d1j2ga2
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	d1j2gb1
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	d1j2gb2
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	d1j2gc1
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	d1j2gc2
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	d1j2gd1
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	d1j2gd2
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 (4 domains)

结构域编号 domain_id	1j2gA00
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	1j2gB00
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	1j2gC00
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	1j2gD00
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 (1)

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晶胞边长 a length_a	133.390 Å
晶胞边长 b length_b	144.410 Å
晶胞边长 c length_c	78.785 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	16

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	48.010 Å
R 因子 r_factor	0.1823
R_work r_work	0.1804
R_free r_free	0.2181

fit	/app/data/saxs_computation/j2/1j2g/1j2g.fit
pddf	/app/data/pr_computation/j2/1j2g/1j2g.pr.out
profile	/app/data/saxs_computation/j2/1j2g/1j2g.dat

Crystal structure of Urate oxidase from Bacillus SP. TB-90 co-crystallized with 8-Azaxanthine

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