2cj9
Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with an analog of seryladenylate
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 | 2cj9 |
| 沉积日期 deposition_date | 2006-03-29 |
| 结构标题 title | Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with an analog of seryladenylate |
| 关键词 keywords | LIGASE, ZINC ION, SERYLADENYLATE, TRNA SYNTHETASE; LIGASE |
| 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 | 34.70 Å |
| 回转半径 Rg (电子) rg_electron | 34.31 Å |
| 零角强度 I(0) i0 | 195525000.00 |
| 分子量 molecular_weight | 112990.0 kDa |
| 排除体积 excluded_volume | 141600 ų |
| 包络体积 envelope_volume | 184570 ų |
| 水化壳体积 shell_volume | 45169 ų |
| 包络直径 envelope_diameter | 122.6 Å |
| 壳层 Rg shell_rg | 39.94 Å |
| 包络 Rg envelope_rg | 35.63 Å |
| 形状 Rg shape_rg | 34.30 Å |
| 总 Rg total_rg | 34.76 Å |
| 总原子数 total_atoms | 7961 |
| 残基数 n_residues | 970 |
| 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 | 115.0 Å |
| Rg (实空间) rg_real | 34.77 Å |
| Rg 误差 (实空间) rg_real_error | 0.94 Å |
| I(0) (实空间) i0_real | 1.9550e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.9760e+06 |
| Rg (倒空间) rg_reciprocal | 34.73 Å |
| I(0) (倒空间) i0_reciprocal | 195500000.0000 |
| 解质量估计 total_estimate | 0.6825 |
| 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 | 37.5 Å |
| 偏度 Skewness skewness | 0.397 |
| 峰度 Kurtosis kurtosis | -0.413 |
| 角度范围 angular_range | — – 0.2300 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 72730000.0000 |
| 实空间数据点数 n_real_points | 47 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.863; Stabil: 1.000; Sysdev: 0.122; Positv: 1.000; Valcen: 0.983; Smooth: 0.929 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (5)
6. 折叠分类 (SCOP + CATH) 4 domains
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 2cj9A01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 1920 — |
| 结构域编号 domain_id | 2cj9A02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 930 — BirA Bifunctional Protein; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Bira Bifunctional Protein; Domain 2 |
| 结构域编号 domain_id | 2cj9B01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 1920 — |
| 结构域编号 domain_id | 2cj9B02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 930 — BirA Bifunctional Protein; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Bira Bifunctional Protein; Domain 2 |