2f8s
Crystal structure of Aa-Ago with externally-bound siRNA
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 | 2f8s |
| 沉积日期 deposition_date | 2005-12-03 |
| 结构标题 title | Crystal structure of Aa-Ago with externally-bound siRNA |
| 关键词 keywords | Argonaute, siRNA, RISC loading complex, RNA BINDING PROTEIN-RNA COMPLEX; RNA BINDING PROTEIN/RNA |
| 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 | 44.32 Å |
| 回转半径 Rg (电子) rg_electron | 42.63 Å |
| 零角强度 I(0) i0 | 474309000.00 |
| 分子量 molecular_weight | 180070.0 kDa |
| 排除体积 excluded_volume | 226420 ų |
| 包络体积 envelope_volume | 319910 ų |
| 水化壳体积 shell_volume | 63525 ų |
| 包络直径 envelope_diameter | 169.0 Å |
| 壳层 Rg shell_rg | 46.77 Å |
| 包络 Rg envelope_rg | 42.54 Å |
| 形状 Rg shape_rg | 42.51 Å |
| 总 Rg total_rg | 43.27 Å |
| 总原子数 total_atoms | 12658 |
| 残基数 n_residues | 1452 |
| 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 | 160.7 Å |
| Rg (实空间) rg_real | 44.46 Å |
| Rg 误差 (实空间) rg_real_error | 1.60 Å |
| I(0) (实空间) i0_real | 4.7430e+08 |
| I(0) 误差 (实空间) i0_real_error | 9.0240e+06 |
| Rg (倒空间) rg_reciprocal | 44.32 Å |
| I(0) (倒空间) i0_reciprocal | 474200000.0000 |
| 解质量估计 total_estimate | 0.6309 |
| 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 | 44.6 Å |
| 偏度 Skewness skewness | 0.430 |
| 峰度 Kurtosis kurtosis | -0.245 |
| 角度范围 angular_range | — – 0.1800 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 46840000.0000 |
| 实空间数据点数 n_real_points | 37 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.742; Stabil: 1.000; Sysdev: 0.032; Positv: 1.000; Valcen: 0.927; Smooth: 0.947 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (3)
6. 折叠分类 (SCOP + CATH) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d2f8sa1 |
| 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 | d2f8sa3 |
| 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 | d2f8sa4 |
| 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 | d2f8sb1 |
| 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 | d2f8sb3 |
| 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 | d2f8sb4 |
| 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 |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 2f8sA02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 340 — PAZ domain fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — PAZ domain superfamily |
| 结构域编号 domain_id | 2f8sA03 |
| 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 | 2f8sA04 |
| 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 | 2f8sB02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 340 — PAZ domain fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — PAZ domain superfamily |
| 结构域编号 domain_id | 2f8sB03 |
| 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 | 2f8sB04 |
| 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 |