1q3b
Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli: The R252A mutant at 2.05 resolution.
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 | 1q3b |
| 沉积日期 deposition_date | 2003-07-29 |
| 结构标题 title | Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli: The R252A mutant at 2.05 resolution. |
| 关键词 keywords | 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 | 22.60 Å |
| 回转半径 Rg (电子) rg_electron | 21.72 Å |
| 零角强度 I(0) i0 | 15274300.00 |
| 分子量 molecular_weight | 29447.0 kDa |
| 排除体积 excluded_volume | 36885 ų |
| 包络体积 envelope_volume | 44453 ų |
| 水化壳体积 shell_volume | 18244 ų |
| 包络直径 envelope_diameter | 74.3 Å |
| 壳层 Rg shell_rg | 26.86 Å |
| 包络 Rg envelope_rg | 21.70 Å |
| 形状 Rg shape_rg | 21.68 Å |
| 总 Rg total_rg | 22.56 Å |
| 总原子数 total_atoms | 2077 |
| 残基数 n_residues | 259 |
| 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 | 72.2 Å |
| Rg (实空间) rg_real | 22.68 Å |
| Rg 误差 (实空间) rg_real_error | 0.41 Å |
| I(0) (实空间) i0_real | 1.5270e+07 |
| I(0) 误差 (实空间) i0_real_error | 2.0090e+05 |
| Rg (倒空间) rg_reciprocal | 22.67 Å |
| I(0) (倒空间) i0_reciprocal | 15270000.0000 |
| 解质量估计 total_estimate | 0.8920 |
| 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 | 23.0 Å |
| 偏度 Skewness skewness | 0.408 |
| 峰度 Kurtosis kurtosis | -0.477 |
| 角度范围 angular_range | — – 0.3500 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 2350000.0000 |
| 实空间数据点数 n_real_points | 67 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.883; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.986 |
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) 5 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d1q3ba1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.156 — S13-like H2TH domain |
| 超家族 Superfamily superfamily | a.156.1 — S13-like H2TH domain |
| 家族 Family family | a.156.1.2 — Middle domain of MutM-like DNA repair proteins |
| 结构域编号 domain_id | d1q3ba2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.113 — N-terminal domain of MutM-like DNA repair proteins |
| 超家族 Superfamily superfamily | b.113.1 — N-terminal domain of MutM-like DNA repair proteins |
| 家族 Family family | b.113.1.1 — N-terminal domain of MutM-like DNA repair proteins |
| 结构域编号 domain_id | d1q3ba3 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.39 — Glucocorticoid receptor-like (DNA-binding domain) |
| 超家族 Superfamily superfamily | g.39.1 — Glucocorticoid receptor-like (DNA-binding domain) |
| 家族 Family family | g.39.1.8 — C-terminal, Zn-finger domain of MutM-like DNA repair proteins |
CATH v4.4 (2 domains)
| 结构域编号 domain_id | 1q3bA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 190 — N-terminal domain of MutM-like DNA repair proteins |
| 同源超家族 H-superfamily homologous superfamily | 10 — MutM-like, N-terminal |
| 结构域编号 domain_id | 1q3bA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 8 — Helicase, Ruva Protein; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 50 — |