1rak
Bacterial cytosine deaminase D314S mutant bound to 5-fluoro-4-(S)-hydroxyl-3,4-dihydropyrimidine.
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 | 1rak |
| 沉积日期 deposition_date | 2003-10-31 |
| 结构标题 title | Bacterial cytosine deaminase D314S mutant bound to 5-fluoro-4-(S)-hydroxyl-3,4-dihydropyrimidine. |
| 关键词 keywords | CYTOSINE DEAMINASE, ALPHA-BETA BARREL, HEXAMER, CONFORMATIONAL CHANGE, D314S mutant, 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 | 22.97 Å |
| 回转半径 Rg (电子) rg_electron | 22.04 Å |
| 零角强度 I(0) i0 | 38236900.00 |
| 分子量 molecular_weight | 47384.0 kDa |
| 排除体积 excluded_volume | 59085 ų |
| 包络体积 envelope_volume | 68433 ų |
| 水化壳体积 shell_volume | 25624 ų |
| 包络直径 envelope_diameter | 80.9 Å |
| 壳层 Rg shell_rg | 29.17 Å |
| 包络 Rg envelope_rg | 22.68 Å |
| 形状 Rg shape_rg | 22.05 Å |
| 总 Rg total_rg | 22.83 Å |
| 总原子数 total_atoms | 3339 |
| 残基数 n_residues | 423 |
| 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 | 78.8 Å |
| Rg (实空间) rg_real | 22.93 Å |
| Rg 误差 (实空间) rg_real_error | 0.51 Å |
| I(0) (实空间) i0_real | 3.8240e+07 |
| I(0) 误差 (实空间) i0_real_error | 5.5330e+05 |
| Rg (倒空间) rg_reciprocal | 22.94 Å |
| I(0) (倒空间) i0_reciprocal | 38240000.0000 |
| 解质量估计 total_estimate | 0.6754 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 26.7 Å |
| 偏度 Skewness skewness | 0.343 |
| 峰度 Kurtosis kurtosis | -0.237 |
| 角度范围 angular_range | — – 0.3450 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 11530000.0000 |
| 实空间数据点数 n_real_points | 66 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.772; Stabil: 1.000; Sysdev: 0.171; Positv: 1.000; Valcen: 0.991; Smooth: 0.954 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (5)
6. 折叠分类 (SCOP + CATH) 4 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d1raka1 |
| 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.92.1.2 — Cytosine deaminase |
| 结构域编号 domain_id | d1raka2 |
| 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.1.9.5 — Cytosine deaminase catalytic domain |
CATH v4.4 (2 domains)
| 结构域编号 domain_id | 1rakA01 |
| 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 | 1rakA02 |
| 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 |