2egv
Crystal structure of rRNA methyltransferase with SAM ligand
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 | 2egv |
| 沉积日期 deposition_date | 2007-03-02 |
| 结构标题 title | Crystal structure of rRNA methyltransferase with SAM ligand |
| 关键词 keywords | ;RsmE, methyltransferase, rRNA modification, PUA domain, m3U, SAM, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, RNA methyltransferase ;; RNA methyltransferase |
| 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 | 25.23 Å |
| 回转半径 Rg (电子) rg_electron | 24.05 Å |
| 零角强度 I(0) i0 | 45830400.00 |
| 分子量 molecular_weight | 54165.0 kDa |
| 排除体积 excluded_volume | 68693 ų |
| 包络体积 envelope_volume | 82149 ų |
| 水化壳体积 shell_volume | 28435 ų |
| 包络直径 envelope_diameter | 84.5 Å |
| 壳层 Rg shell_rg | 31.46 Å |
| 包络 Rg envelope_rg | 24.34 Å |
| 形状 Rg shape_rg | 24.04 Å |
| 总 Rg total_rg | 24.95 Å |
| 总原子数 total_atoms | 3806 |
| 残基数 n_residues | 458 |
| 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 | 83.8 Å |
| Rg (实空间) rg_real | 25.20 Å |
| Rg 误差 (实空间) rg_real_error | 0.68 Å |
| I(0) (实空间) i0_real | 4.5830e+07 |
| I(0) 误差 (实空间) i0_real_error | 6.4680e+05 |
| Rg (倒空间) rg_reciprocal | 25.21 Å |
| I(0) (倒空间) i0_reciprocal | 45830000.0000 |
| 解质量估计 total_estimate | 0.8865 |
| 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 | 30.6 Å |
| 偏度 Skewness skewness | 0.332 |
| 峰度 Kurtosis kurtosis | -0.221 |
| 角度范围 angular_range | — – 0.3150 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 11130000.0000 |
| 实空间数据点数 n_real_points | 64 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.853; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.983 |
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) 4 domains
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 2egvA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 240 — Ribosomal Protein L25; Chain P |
| 同源超家族 H-superfamily homologous superfamily | 20 — Hypothetical PUA domain-like; domain 1 |
| 结构域编号 domain_id | 2egvA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1280 — Alpha/beta knot |
| 同源超家族 H-superfamily homologous superfamily | 10 — SPOUT methyltransferase, trefoil knot domain |
| 结构域编号 domain_id | 2egvB01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 240 — Ribosomal Protein L25; Chain P |
| 同源超家族 H-superfamily homologous superfamily | 20 — Hypothetical PUA domain-like; domain 1 |
| 结构域编号 domain_id | 2egvB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1280 — Alpha/beta knot |
| 同源超家族 H-superfamily homologous superfamily | 10 — SPOUT methyltransferase, trefoil knot domain |