2deu
Cocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Glu in the adenylated intermediate state
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 | 2deu |
| 沉积日期 deposition_date | 2006-02-17 |
| 结构标题 title | Cocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Glu in the adenylated intermediate state |
| 关键词 keywords | Protein-RNA complex, adenylated intermediate of RNA, Transferase-RNA COMPLEX; Transferase/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 | 39.82 Å |
| 回转半径 Rg (电子) rg_electron | 39.98 Å |
| 零角强度 I(0) i0 | 408531000.00 |
| 分子量 molecular_weight | 129600.0 kDa |
| 排除体积 excluded_volume | 146660 ų |
| 包络体积 envelope_volume | 225130 ų |
| 水化壳体积 shell_volume | 45773 ų |
| 包络直径 envelope_diameter | 147.0 Å |
| 壳层 Rg shell_rg | 47.63 Å |
| 包络 Rg envelope_rg | 38.91 Å |
| 形状 Rg shape_rg | 40.02 Å |
| 总 Rg total_rg | 40.21 Å |
| 总原子数 total_atoms | 8908 |
| 残基数 n_residues | 874 |
| 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 | 133.4 Å |
| Rg (实空间) rg_real | 39.72 Å |
| Rg 误差 (实空间) rg_real_error | 1.19 Å |
| I(0) (实空间) i0_real | 4.0850e+08 |
| I(0) 误差 (实空间) i0_real_error | 7.7270e+06 |
| Rg (倒空间) rg_reciprocal | 39.79 Å |
| I(0) (倒空间) i0_reciprocal | 408600000.0000 |
| 解质量估计 total_estimate | 0.8960 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 53.4 Å |
| 偏度 Skewness skewness | 0.138 |
| 峰度 Kurtosis kurtosis | -0.616 |
| 角度范围 angular_range | — – 0.2000 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 14460000.0000 |
| 实空间数据点数 n_real_points | 41 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.975 |
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) 6 domains
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 2deuA01 |
| 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 | 620 — HUPs |
| 结构域编号 domain_id | 2deuA02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 30 — SH3 type barrels. |
| 同源超家族 H-superfamily homologous superfamily | 280 — Adenine nucleotide alpha hydrolases-like domains |
| 结构域编号 domain_id | 2deuA03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 30 — Elongation Factor Tu (Ef-tu); domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Translation factors |
| 结构域编号 domain_id | 2deuB01 |
| 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 | 620 — HUPs |
| 结构域编号 domain_id | 2deuB02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 30 — SH3 type barrels. |
| 同源超家族 H-superfamily homologous superfamily | 280 — Adenine nucleotide alpha hydrolases-like domains |
| 结构域编号 domain_id | 2deuB03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 30 — Elongation Factor Tu (Ef-tu); domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Translation factors |