1gkr

L-Hydantoinase (Dihydropyrimidinase) from Arthrobacter aurescens

Method: X-RAY DIFFRACTION D_max: 122.2 Å Quality: EXCELLENT

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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1gkr
沉积日期 deposition_date	2001-08-20
结构标题 title	L-Hydantoinase (Dihydropyrimidinase) from Arthrobacter aurescens
关键词 keywords	HYDROLASE, HYDANTOINASE, DIHYDROPYRIMIDINASE, CYCLIC AMIDASE; HYDROLASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	39.11 Å
回转半径 Rg (电子) rg_electron	38.56 Å
零角强度 I(0) i0	576824000.00
分子量 molecular_weight	195530.0 kDa
排除体积 excluded_volume	244100 Å³
包络体积 envelope_volume	299740 Å³
水化壳体积 shell_volume	61996 Å³
包络直径 envelope_diameter	130.6 Å
壳层 Rg shell_rg	46.69 Å
包络 Rg envelope_rg	38.11 Å
形状 Rg shape_rg	38.56 Å
总 Rg total_rg	38.98 Å
总原子数 total_atoms	13688
残基数 n_residues	1800
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	122.2 Å
Rg (实空间) rg_real	38.91 Å
Rg 误差 (实空间) rg_real_error	0.61 Å
I(0) (实空间) i0_real	5.7680e+08
I(0) 误差 (实空间) i0_real_error	7.7500e+06
Rg (倒空间) rg_reciprocal	39.04 Å
I(0) (倒空间) i0_reciprocal	576900000.0000
解质量估计 total_estimate	0.9007
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	55.0 Å
偏度 Skewness skewness	0.144
峰度 Kurtosis kurtosis	-0.542
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	315900000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.898

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	NON-ATP DEPENDENT L-SELECTIVE HYDANTOINASE
分子量 formula_weight	49693.4 kDa
EC 编号 ec_number	3.5.2.2
来源方法 src_method	nat
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	14196

MFDVIVKNCRLVSSDGITEADILVKDGKVAAISADTSDVEASRTIDAGGKFVMPGVVDEHVHIIDMDLKNRYGRFELDSESAAVGGITTIIEMPITFPPTTTLDAFLEKKKQAGQRLKVDFALYGGGVPGNLPEIRKMHDAGAVGFKSMMAASVPGMFDAVSDGELFEIFQEIAACGSVIVVHAENETIIQALQKQIKAAGGKDMAAYEASQPVFQENEAIQRALLLQKEAGCRLIVLHVSNPDGVELIHQAQSEGQDVHCESGPQYLNITTDDAERIGPYMKVAPPVRSAEMNIRLWEQLENGLIDTLGSDHGGHPVEDKEPGWKDVWKAGNGALGLETSLPMMLTNGVNKGRLSLERLVEVMCEKPAKLFGIYPQKGTLQVGSDADLLILDLDIDTKVDASQFRSLHKYSPFDGMPVTGAPVLTMVRGTVVAEKGEVLVEQGFGQFVTRRNYEASK

Entity 2 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

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	508

▼

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1gkra1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
超家族 Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
家族 Family family	b.92.1.3 — Hydantoinase (dihydropyrimidinase)

结构域编号 domain_id	d1gkra2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
家族 Family family	c.1.9.6 — Hydantoinase (dihydropyrimidinase), catalytic domain

结构域编号 domain_id	d1gkrb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
超家族 Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
家族 Family family	b.92.1.3 — Hydantoinase (dihydropyrimidinase)

结构域编号 domain_id	d1gkrb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
家族 Family family	c.1.9.6 — Hydantoinase (dihydropyrimidinase), catalytic domain

结构域编号 domain_id	d1gkrc1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
超家族 Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
家族 Family family	b.92.1.3 — Hydantoinase (dihydropyrimidinase)

结构域编号 domain_id	d1gkrc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
家族 Family family	c.1.9.6 — Hydantoinase (dihydropyrimidinase), catalytic domain

结构域编号 domain_id	d1gkrd1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
超家族 Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
家族 Family family	b.92.1.3 — Hydantoinase (dihydropyrimidinase)

结构域编号 domain_id	d1gkrd2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
家族 Family family	c.1.9.6 — Hydantoinase (dihydropyrimidinase), catalytic domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1gkrA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	40 — Urease, subunit C; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Urease, subunit C, domain 1

结构域编号 domain_id	1gkrA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	140 — Metal-dependent hydrolases

结构域编号 domain_id	1gkrB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	40 — Urease, subunit C; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Urease, subunit C, domain 1

结构域编号 domain_id	1gkrB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	140 — Metal-dependent hydrolases

结构域编号 domain_id	1gkrC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	40 — Urease, subunit C; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Urease, subunit C, domain 1

结构域编号 domain_id	1gkrC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	140 — Metal-dependent hydrolases

结构域编号 domain_id	1gkrD01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	40 — Urease, subunit C; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Urease, subunit C, domain 1

结构域编号 domain_id	1gkrD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	140 — Metal-dependent hydrolases

▶

7. 引用文献 (2)

▶

晶胞边长 a length_a	111.500 Å
晶胞边长 b length_b	74.300 Å
晶胞边长 c length_c	146.900 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	106.57 °
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	2.600 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2240
R_work r_work	0.2240
R_free r_free	0.2440

fit	/app/data/saxs_computation/gk/1gkr/1gkr.fit
pddf	/app/data/pr_computation/gk/1gkr/1gkr.pr.out
profile	/app/data/saxs_computation/gk/1gkr/1gkr.dat

L-Hydantoinase (Dihydropyrimidinase) from Arthrobacter aurescens

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