1q8i
Crystal structure of ESCHERICHIA coli DNA Polymerase II
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 | 1q8i |
| 沉积日期 deposition_date | 2003-08-21 |
| 结构标题 title | Crystal structure of ESCHERICHIA coli DNA Polymerase II |
| 关键词 keywords | ;DNA Polymerase II, Structural Genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, TRANSFERASE ;; TRANSFERASE |
| 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 | 32.26 Å |
| 回转半径 Rg (电子) rg_electron | 31.26 Å |
| 零角强度 I(0) i0 | 102578000.00 |
| 分子量 molecular_weight | 80803.0 kDa |
| 排除体积 excluded_volume | 101380 ų |
| 包络体积 envelope_volume | 135800 ų |
| 水化壳体积 shell_volume | 36715 ų |
| 包络直径 envelope_diameter | 102.1 Å |
| 壳层 Rg shell_rg | 38.05 Å |
| 包络 Rg envelope_rg | 30.67 Å |
| 形状 Rg shape_rg | 31.26 Å |
| 总 Rg total_rg | 31.90 Å |
| 总原子数 total_atoms | 5709 |
| 残基数 n_residues | 708 |
| 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 | 97.5 Å |
| Rg (实空间) rg_real | 32.14 Å |
| Rg 误差 (实空间) rg_real_error | 0.70 Å |
| I(0) (实空间) i0_real | 1.0260e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.4960e+06 |
| Rg (倒空间) rg_reciprocal | 32.20 Å |
| I(0) (倒空间) i0_reciprocal | 102600000.0000 |
| 解质量估计 total_estimate | 0.9048 |
| 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 | 39.8 Å |
| 偏度 Skewness skewness | 0.126 |
| 峰度 Kurtosis kurtosis | -0.714 |
| 角度范围 angular_range | — – 0.2450 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 15560000.0000 |
| 实空间数据点数 n_real_points | 50 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.983; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.815 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (2)
6. 折叠分类 (SCOP + CATH) 8 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d1q8ia1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.55 — Ribonuclease H-like motif |
| 超家族 Superfamily superfamily | c.55.3 — Ribonuclease H-like |
| 家族 Family family | c.55.3.5 — DnaQ-like 3'-5' exonuclease |
| 结构域编号 domain_id | d1q8ia2 |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.8 — DNA/RNA polymerases |
| 超家族 Superfamily superfamily | e.8.1 — DNA/RNA polymerases |
| 家族 Family family | e.8.1.1 — DNA polymerase I |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1q8iA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P) |
| 同源超家族 H-superfamily homologous superfamily | 590 — DNA polymerase B, N domain, beta-barrel |
| 结构域编号 domain_id | 1q8iA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 2250 — B family DNA polymerase, N domain, alpha/beta motif |
| 结构域编号 domain_id | 1q8iA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 420 — Nucleotidyltransferase; domain 5 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ribonuclease H-like superfamily/Ribonuclease H |
| 结构域编号 domain_id | 1q8iA04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1600 — Palm domain of DNA polymerase |
| 同源超家族 H-superfamily homologous superfamily | 10 — B family DNA polymerase, palm domain |
| 结构域编号 domain_id | 1q8iA05 |
| 类 Class class | 6 — Special |
| 架构 Architecture architecture | 10 — Helix non-globular |
| 拓扑 Topology topology | 140 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 1130 — |
| 结构域编号 domain_id | 1q8iA06 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 287 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 690 — B family DNA polymerase, finger domain |