1r6z
The Crystal Structure of the Argonaute2 PAZ domain (as a MBP fusion)
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 | 1r6z |
| 沉积日期 deposition_date | 2003-10-17 |
| 结构标题 title | The Crystal Structure of the Argonaute2 PAZ domain (as a MBP fusion) |
| 关键词 keywords | deviant OB fold, RNAi, GENE REGULATION; 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 | 42.53 Å |
| 回转半径 Rg (电子) rg_electron | 41.84 Å |
| 零角强度 I(0) i0 | 395434000.00 |
| 分子量 molecular_weight | 167040.0 kDa |
| 排除体积 excluded_volume | 210770 ų |
| 包络体积 envelope_volume | 300000 ų |
| 水化壳体积 shell_volume | 60055 ų |
| 包络直径 envelope_diameter | 138.5 Å |
| 壳层 Rg shell_rg | 46.64 Å |
| 包络 Rg envelope_rg | 41.50 Å |
| 形状 Rg shape_rg | 41.77 Å |
| 总 Rg total_rg | 42.37 Å |
| 总原子数 total_atoms | 11777 |
| 残基数 n_residues | 1494 |
| 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 | 133.9 Å |
| Rg (实空间) rg_real | 42.45 Å |
| Rg 误差 (实空间) rg_real_error | 1.06 Å |
| I(0) (实空间) i0_real | 3.9540e+08 |
| I(0) 误差 (实空间) i0_real_error | 6.4340e+06 |
| Rg (倒空间) rg_reciprocal | 42.53 Å |
| I(0) (倒空间) i0_reciprocal | 395500000.0000 |
| 解质量估计 total_estimate | 0.8782 |
| 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 | 54.3 Å |
| 偏度 Skewness skewness | 0.243 |
| 峰度 Kurtosis kurtosis | -0.423 |
| 角度范围 angular_range | — – 0.1850 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 28120000.0000 |
| 实空间数据点数 n_real_points | 38 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.653 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (4)
6. 折叠分类 (SCOP + CATH) 15 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1r6za1 |
| 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 | d1r6za2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.94 — Periplasmic binding protein-like II |
| 超家族 Superfamily superfamily | c.94.1 — Periplasmic binding protein-like II |
| 家族 Family family | c.94.1.1 — Phosphate binding protein-like |
| 结构域编号 domain_id | d1r6zp1 |
| 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 | d1r6zp2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.94 — Periplasmic binding protein-like II |
| 超家族 Superfamily superfamily | c.94.1 — Periplasmic binding protein-like II |
| 家族 Family family | c.94.1.1 — Phosphate binding protein-like |
| 结构域编号 domain_id | d1r6zz1 |
| 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 | d1r6zz2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.94 — Periplasmic binding protein-like II |
| 超家族 Superfamily superfamily | c.94.1 — Periplasmic binding protein-like II |
| 家族 Family family | c.94.1.1 — Phosphate binding protein-like |
CATH v4.4 (9 domains)
| 结构域编号 domain_id | 1r6zA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 190 — D-Maltodextrin-Binding Protein; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Periplasmic binding protein-like II |
| 结构域编号 domain_id | 1r6zA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 190 — D-Maltodextrin-Binding Protein; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Periplasmic binding protein-like II |
| 结构域编号 domain_id | 1r6zA03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 170 — Beta Complex |
| 拓扑 Topology topology | 260 — paz domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — paz domain |
| 结构域编号 domain_id | 1r6zP01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 190 — D-Maltodextrin-Binding Protein; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Periplasmic binding protein-like II |
| 结构域编号 domain_id | 1r6zP02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 190 — D-Maltodextrin-Binding Protein; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Periplasmic binding protein-like II |
| 结构域编号 domain_id | 1r6zP03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 170 — Beta Complex |
| 拓扑 Topology topology | 260 — paz domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — paz domain |
| 结构域编号 domain_id | 1r6zZ01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 190 — D-Maltodextrin-Binding Protein; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Periplasmic binding protein-like II |
| 结构域编号 domain_id | 1r6zZ02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 190 — D-Maltodextrin-Binding Protein; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Periplasmic binding protein-like II |
| 结构域编号 domain_id | 1r6zZ03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 170 — Beta Complex |
| 拓扑 Topology topology | 260 — paz domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — paz domain |