2dra
Complex structure of CCA-adding enzyme with tRNAminiDCC and ATP
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 | 2dra |
| 沉积日期 deposition_date | 2006-06-08 |
| 结构标题 title | Complex structure of CCA-adding enzyme with tRNAminiDCC and ATP |
| 关键词 keywords | protein-rna complex, 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 | 27.74 Å |
| 回转半径 Rg (电子) rg_electron | 27.53 Å |
| 零角强度 I(0) i0 | 80573000.00 |
| 分子量 molecular_weight | 63013.0 kDa |
| 排除体积 excluded_volume | 75621 ų |
| 包络体积 envelope_volume | 99645 ų |
| 水化壳体积 shell_volume | 30824 ų |
| 包络直径 envelope_diameter | 100.0 Å |
| 壳层 Rg shell_rg | 34.02 Å |
| 包络 Rg envelope_rg | 27.47 Å |
| 形状 Rg shape_rg | 27.53 Å |
| 总 Rg total_rg | 28.12 Å |
| 总原子数 total_atoms | 4391 |
| 残基数 n_residues | 471 |
| 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 | 94.2 Å |
| Rg (实空间) rg_real | 27.77 Å |
| Rg 误差 (实空间) rg_real_error | 0.77 Å |
| I(0) (实空间) i0_real | 8.0570e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.1480e+06 |
| Rg (倒空间) rg_reciprocal | 27.76 Å |
| I(0) (倒空间) i0_reciprocal | 80570000.0000 |
| 解质量估计 total_estimate | 0.8058 |
| 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 | 92.5 Å |
| 偏度 Skewness skewness | 0.385 |
| 峰度 Kurtosis kurtosis | -0.211 |
| 角度范围 angular_range | — – 0.2850 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 13000000.0000 |
| 实空间数据点数 n_real_points | 58 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (6)
6. 折叠分类 (SCOP + CATH) 7 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d2draa1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.160 — PAP/OAS1 substrate-binding domain |
| 超家族 Superfamily superfamily | a.160.1 — PAP/OAS1 substrate-binding domain |
| 家族 Family family | a.160.1.3 — Archaeal tRNA CCA-adding enzyme substrate-binding domain |
| 结构域编号 domain_id | d2draa2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.218 — Nucleotidyltransferase |
| 超家族 Superfamily superfamily | d.218.1 — Nucleotidyltransferase |
| 家族 Family family | d.218.1.7 — Archaeal tRNA CCA-adding enzyme catalytic domain |
| 结构域编号 domain_id | d2draa3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.16 — PAP/Archaeal CCA-adding enzyme, C-terminal domain |
| 家族 Family family | d.58.16.2 — Archaeal tRNA CCA-adding enzyme |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 2draA01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1410 — Poly(a)-polymerase, middle domain |
| 同源超家族 H-superfamily homologous superfamily | 30 — CCA tRNA nucleotidyltransferase, domain 2 |
| 结构域编号 domain_id | 2draA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 460 — Beta Polymerase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Beta Polymerase, domain 2 |
| 结构域编号 domain_id | 2draA03 |
| 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 | 590 — Poly(A) polymerase predicted RNA binding domain |
| 结构域编号 domain_id | 2draA04 |
| 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 | 1550 — Archaeal tRNA CCA-adding enzyme catalytic domain |