1yny
Molecular Structure of D-Hydantoinase from a Bacillus sp. AR9: Evidence for mercury inhibition
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
| 条目编号 entry_id | 1yny |
| 沉积日期 deposition_date | 2005-01-26 |
| 结构标题 title | Molecular Structure of D-Hydantoinase from a Bacillus sp. AR9: Evidence for mercury inhibition |
| 关键词 keywords | TIM-barrel; hydantoinase; binuclear metal-binding; hydrolase, HYDROLASE; 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 | 64.09 Å |
| 回转半径 Rg (电子) rg_electron | 64.84 Å |
| 零角强度 I(0) i0 | 139286000.00 |
| 分子量 molecular_weight | 100110.0 kDa |
| 排除体积 excluded_volume | 125220 ų |
| 包络体积 envelope_volume | 209940 ų |
| 水化壳体积 shell_volume | 26348 ų |
| 包络直径 envelope_diameter | 182.3 Å |
| 壳层 Rg shell_rg | 75.71 Å |
| 包络 Rg envelope_rg | 58.92 Å |
| 形状 Rg shape_rg | 64.81 Å |
| 总 Rg total_rg | 65.11 Å |
| 总原子数 total_atoms | 7051 |
| 残基数 n_residues | 914 |
| 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/ų |
| 壳层衬度 contrast_shell | 0.0300 e/ų |
| 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 | 204.9 Å |
| Rg (实空间) rg_real | 65.05 Å |
| Rg 误差 (实空间) rg_real_error | 3.26 Å |
| I(0) (实空间) i0_real | 1.3930e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.1710e+06 |
| Rg (倒空间) rg_reciprocal | 62.99 Å |
| I(0) (倒空间) i0_reciprocal | 138800000.0000 |
| 解质量估计 total_estimate | 0.3082 |
| 解质量评级 solution_quality | SUSPICIOUS a SUSPICIOUS solution |
| P(r) 峰数 n_peaks | 3 |
| 主峰位置 r_peak_primary | 25.6 Å |
| 偏度 Skewness skewness | 0.059 |
| 峰度 Kurtosis kurtosis | -1.729 |
| 角度范围 angular_range | — – 0.1200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 1764000.0000 |
| 实空间数据点数 n_real_points | 25 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.000; Stabil: 1.000; Sysdev: 0.000; Positv: 1.000; Valcen: 0.002; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (3)
6. 折叠分类 (SCOP + CATH) 8 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1ynya1 |
| 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 | d1ynya2 |
| 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 | d1ynyb1 |
| 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 | d1ynyb2 |
| 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 (4 domains)
| 结构域编号 domain_id | 1ynyA01 |
| 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 | 1ynyA02 |
| 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 | 1ynyB01 |
| 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 | 1ynyB02 |
| 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 |