2i9g
DNA Polymerase Beta with a Benzo[c]phenanthrene diol epoxide adducted guanine base
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 | 2i9g |
| 沉积日期 deposition_date | 2006-09-05 |
| 结构标题 title | DNA Polymerase Beta with a Benzo[c]phenanthrene diol epoxide adducted guanine base |
| 关键词 keywords | Mutagenesis, Base Excision Repair, Nucleotidyl Transferase, DNA Adduct, Transferase-DNA COMPLEX; Transferase/DNA |
| 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 | 23.79 Å |
| 回转半径 Rg (电子) rg_electron | 23.05 Å |
| 零角强度 I(0) i0 | 46625700.00 |
| 分子量 molecular_weight | 46927.0 kDa |
| 排除体积 excluded_volume | 56139 ų |
| 包络体积 envelope_volume | 72620 ų |
| 水化壳体积 shell_volume | 26162 ų |
| 包络直径 envelope_diameter | 75.2 Å |
| 壳层 Rg shell_rg | 30.18 Å |
| 包络 Rg envelope_rg | 22.90 Å |
| 形状 Rg shape_rg | 23.03 Å |
| 总 Rg total_rg | 23.87 Å |
| 总原子数 total_atoms | 3263 |
| 残基数 n_residues | 355 |
| 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 | 23.62 Å |
| Rg 误差 (实空间) rg_real_error | 0.38 Å |
| I(0) (实空间) i0_real | 4.6630e+07 |
| I(0) 误差 (实空间) i0_real_error | 6.8290e+05 |
| Rg (倒空间) rg_reciprocal | 23.66 Å |
| I(0) (倒空间) i0_reciprocal | 46630000.0000 |
| 解质量估计 total_estimate | 0.9080 |
| 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 | 31.6 Å |
| 偏度 Skewness skewness | 0.079 |
| 峰度 Kurtosis kurtosis | -0.483 |
| 角度范围 angular_range | — – 0.3350 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 4402000.0000 |
| 实空间数据点数 n_real_points | 65 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.998 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (8)
6. 折叠分类 (SCOP + CATH) 7 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d2i9ga1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.60 — SAM domain-like |
| 超家族 Superfamily superfamily | a.60.6 — DNA polymerase beta, N-terminal domain-like |
| 家族 Family family | a.60.6.1 — DNA polymerase beta, N-terminal domain-like |
| 结构域编号 domain_id | d2i9ga2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.60 — SAM domain-like |
| 超家族 Superfamily superfamily | a.60.12 — PsbU/PolX domain-like |
| 家族 Family family | a.60.12.1 — DNA polymerase beta-like, second domain |
| 结构域编号 domain_id | d2i9ga3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.218 — Nucleotidyltransferase |
| 超家族 Superfamily superfamily | d.218.1 — Nucleotidyltransferase |
| 家族 Family family | d.218.1.2 — DNA polymerase beta-like |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 2i9gA01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 150 — DNA polymerase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 110 — DNA polymerase beta, N-terminal domain-like |
| 结构域编号 domain_id | 2i9gA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 150 — DNA polymerase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — 5' to 3' exonuclease, C-terminal subdomain |
| 结构域编号 domain_id | 2i9gA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 460 — Beta Polymerase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Beta Polymerase, domain 2 |
| 结构域编号 domain_id | 2i9gA04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 210 — Beta Polymerase; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — DNA polymerase, thumb domain |