1oyr
Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis
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 | 1oyr |
| 沉积日期 deposition_date | 2003-04-07 |
| 结构标题 title | Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis |
| 关键词 keywords | Transferase, tRNA processing; 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 | 35.62 Å |
| 回转半径 Rg (电子) rg_electron | 34.88 Å |
| 零角强度 I(0) i0 | 409247000.00 |
| 分子量 molecular_weight | 159210.0 kDa |
| 排除体积 excluded_volume | 197710 ų |
| 包络体积 envelope_volume | 256440 ų |
| 水化壳体积 shell_volume | 58489 ų |
| 包络直径 envelope_diameter | 103.4 Å |
| 壳层 Rg shell_rg | 43.85 Å |
| 包络 Rg envelope_rg | 34.05 Å |
| 形状 Rg shape_rg | 34.90 Å |
| 总 Rg total_rg | 35.41 Å |
| 总原子数 total_atoms | 11127 |
| 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 | 106.0 Å |
| Rg (实空间) rg_real | 35.38 Å |
| Rg 误差 (实空间) rg_real_error | 0.69 Å |
| I(0) (实空间) i0_real | 4.0920e+08 |
| I(0) 误差 (实空间) i0_real_error | 6.7210e+06 |
| Rg (倒空间) rg_reciprocal | 35.53 Å |
| I(0) (倒空间) i0_reciprocal | 409300000.0000 |
| 解质量估计 total_estimate | 0.9117 |
| 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 | 45.8 Å |
| 偏度 Skewness skewness | 0.032 |
| 峰度 Kurtosis kurtosis | -0.685 |
| 角度范围 angular_range | — – 0.2200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 70020000.0000 |
| 实空间数据点数 n_real_points | 45 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.966; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.970 |
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) 18 domains
SCOP 2.08 (12 domains)
| 结构域编号 domain_id | d1oyra1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.14 — Ribosomal protein S5 domain 2-like |
| 超家族 Superfamily superfamily | d.14.1 — Ribosomal protein S5 domain 2-like |
| 家族 Family family | d.14.1.4 — Ribonuclease PH domain 1-like |
| 结构域编号 domain_id | d1oyra2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.101 — Ribonuclease PH domain 2-like |
| 超家族 Superfamily superfamily | d.101.1 — Ribonuclease PH domain 2-like |
| 家族 Family family | d.101.1.1 — Ribonuclease PH domain 2-like |
| 结构域编号 domain_id | d1oyrb1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.14 — Ribosomal protein S5 domain 2-like |
| 超家族 Superfamily superfamily | d.14.1 — Ribosomal protein S5 domain 2-like |
| 家族 Family family | d.14.1.4 — Ribonuclease PH domain 1-like |
| 结构域编号 domain_id | d1oyrb2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.101 — Ribonuclease PH domain 2-like |
| 超家族 Superfamily superfamily | d.101.1 — Ribonuclease PH domain 2-like |
| 家族 Family family | d.101.1.1 — Ribonuclease PH domain 2-like |
| 结构域编号 domain_id | d1oyrc1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.14 — Ribosomal protein S5 domain 2-like |
| 超家族 Superfamily superfamily | d.14.1 — Ribosomal protein S5 domain 2-like |
| 家族 Family family | d.14.1.4 — Ribonuclease PH domain 1-like |
| 结构域编号 domain_id | d1oyrc2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.101 — Ribonuclease PH domain 2-like |
| 超家族 Superfamily superfamily | d.101.1 — Ribonuclease PH domain 2-like |
| 家族 Family family | d.101.1.1 — Ribonuclease PH domain 2-like |
| 结构域编号 domain_id | d1oyrd1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.14 — Ribosomal protein S5 domain 2-like |
| 超家族 Superfamily superfamily | d.14.1 — Ribosomal protein S5 domain 2-like |
| 家族 Family family | d.14.1.4 — Ribonuclease PH domain 1-like |
| 结构域编号 domain_id | d1oyrd2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.101 — Ribonuclease PH domain 2-like |
| 超家族 Superfamily superfamily | d.101.1 — Ribonuclease PH domain 2-like |
| 家族 Family family | d.101.1.1 — Ribonuclease PH domain 2-like |
| 结构域编号 domain_id | d1oyre1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.14 — Ribosomal protein S5 domain 2-like |
| 超家族 Superfamily superfamily | d.14.1 — Ribosomal protein S5 domain 2-like |
| 家族 Family family | d.14.1.4 — Ribonuclease PH domain 1-like |
| 结构域编号 domain_id | d1oyre2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.101 — Ribonuclease PH domain 2-like |
| 超家族 Superfamily superfamily | d.101.1 — Ribonuclease PH domain 2-like |
| 家族 Family family | d.101.1.1 — Ribonuclease PH domain 2-like |
| 结构域编号 domain_id | d1oyrf1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.14 — Ribosomal protein S5 domain 2-like |
| 超家族 Superfamily superfamily | d.14.1 — Ribosomal protein S5 domain 2-like |
| 家族 Family family | d.14.1.4 — Ribonuclease PH domain 1-like |
| 结构域编号 domain_id | d1oyrf2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.101 — Ribonuclease PH domain 2-like |
| 超家族 Superfamily superfamily | d.101.1 — Ribonuclease PH domain 2-like |
| 家族 Family family | d.101.1.1 — Ribonuclease PH domain 2-like |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1oyrA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 230 — Ribosomal Protein S5; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 70 — GHMP Kinase, N-terminal domain |
| 结构域编号 domain_id | 1oyrB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 230 — Ribosomal Protein S5; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 70 — GHMP Kinase, N-terminal domain |
| 结构域编号 domain_id | 1oyrC01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 230 — Ribosomal Protein S5; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 70 — GHMP Kinase, N-terminal domain |
| 结构域编号 domain_id | 1oyrD01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 230 — Ribosomal Protein S5; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 70 — GHMP Kinase, N-terminal domain |
| 结构域编号 domain_id | 1oyrE01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 230 — Ribosomal Protein S5; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 70 — GHMP Kinase, N-terminal domain |
| 结构域编号 domain_id | 1oyrF01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 230 — Ribosomal Protein S5; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 70 — GHMP Kinase, N-terminal domain |