1u04
Crystal structure of full length Argonaute from Pyrococcus furiosus
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 | 1u04 |
| 沉积日期 deposition_date | 2004-07-12 |
| 结构标题 title | Crystal structure of full length Argonaute from Pyrococcus furiosus |
| 关键词 keywords | RNAi, Silencing, Argonaute, PIWI, PAZ, RISC, Slicer, RNase H, HYDROLASE-GENE REGULATION COMPLEX; HYDROLASE/GENE REGULATION |
| 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 | 29.21 Å |
| 回转半径 Rg (电子) rg_electron | 28.18 Å |
| 零角强度 I(0) i0 | 105639000.00 |
| 分子量 molecular_weight | 84728.0 kDa |
| 排除体积 excluded_volume | 107570 ų |
| 包络体积 envelope_volume | 137450 ų |
| 水化壳体积 shell_volume | 39951 ų |
| 包络直径 envelope_diameter | 95.6 Å |
| 壳层 Rg shell_rg | 36.27 Å |
| 包络 Rg envelope_rg | 27.83 Å |
| 形状 Rg shape_rg | 28.22 Å |
| 总 Rg total_rg | 28.89 Å |
| 总原子数 total_atoms | 5920 |
| 残基数 n_residues | 695 |
| 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 | 89.7 Å |
| Rg (实空间) rg_real | 29.06 Å |
| Rg 误差 (实空间) rg_real_error | 0.59 Å |
| I(0) (实空间) i0_real | 1.0560e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.4010e+06 |
| Rg (倒空间) rg_reciprocal | 29.12 Å |
| I(0) (倒空间) i0_reciprocal | 105600000.0000 |
| 解质量估计 total_estimate | 0.8991 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 88.1 Å |
| 偏度 Skewness skewness | 0.165 |
| 峰度 Kurtosis kurtosis | -0.383 |
| 角度范围 angular_range | — – 0.2700 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 34530000.0000 |
| 实空间数据点数 n_real_points | 55 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.955 |
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) 7 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1u04a1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.34 — SH3-like barrel |
| 超家族 Superfamily superfamily | b.34.14 — PAZ domain |
| 家族 Family family | b.34.14.1 — PAZ domain |
| 结构域编号 domain_id | d1u04a3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.44 — Phosphotyrosine protein phosphatases I-like |
| 超家族 Superfamily superfamily | c.44.3 — PIWI domain N-terminal-like |
| 家族 Family family | c.44.3.1 — PIWI domain N-terminal |
| 结构域编号 domain_id | d1u04a4 |
| 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.55.3.15 — PIWI domain C-terminal |
| 结构域编号 domain_id | d1u04a5 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
CATH v4.4 (3 domains)
| 结构域编号 domain_id | 1u04A02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 70 — Cathepsin B; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 180 — |
| 结构域编号 domain_id | 1u04A03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 2300 — Response regulator |
| 结构域编号 domain_id | 1u04A04 |
| 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 |