1vfg
Crystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an incoming ATP analog
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 | 1vfg |
| 沉积日期 deposition_date | 2004-04-13 |
| 结构标题 title | Crystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an incoming ATP analog |
| 关键词 keywords | TRANSFERASE, RNA, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, 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 | 44.48 Å |
| 回转半径 Rg (电子) rg_electron | 44.21 Å |
| 零角强度 I(0) i0 | 196494000.00 |
| 分子量 molecular_weight | 104050.0 kDa |
| 排除体积 excluded_volume | 125920 ų |
| 包络体积 envelope_volume | 185250 ų |
| 水化壳体积 shell_volume | 37525 ų |
| 包络直径 envelope_diameter | 152.2 Å |
| 壳层 Rg shell_rg | 44.30 Å |
| 包络 Rg envelope_rg | 43.82 Å |
| 形状 Rg shape_rg | 44.13 Å |
| 总 Rg total_rg | 44.43 Å |
| 总原子数 total_atoms | 7240 |
| 残基数 n_residues | 765 |
| 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 | 143.3 Å |
| Rg (实空间) rg_real | 44.98 Å |
| Rg 误差 (实空间) rg_real_error | 1.43 Å |
| I(0) (实空间) i0_real | 1.9650e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.7740e+06 |
| Rg (倒空间) rg_reciprocal | 44.48 Å |
| I(0) (倒空间) i0_reciprocal | 196400000.0000 |
| 解质量估计 total_estimate | 0.7316 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 3 |
| 主峰位置 r_peak_primary | 32.8 Å |
| 偏度 Skewness skewness | 0.415 |
| 峰度 Kurtosis kurtosis | -0.795 |
| 角度范围 angular_range | — – 0.1750 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 10380000.0000 |
| 实空间数据点数 n_real_points | 36 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.638; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.452; Smooth: 0.143 |
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) 9 domains
SCOP 2.08 (5 domains)
| 结构域编号 domain_id | d1vfga1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.173 — Poly A polymerase C-terminal region-like |
| 超家族 Superfamily superfamily | a.173.1 — Poly A polymerase C-terminal region-like |
| 家族 Family family | a.173.1.1 — Poly A polymerase C-terminal region-like |
| 结构域编号 domain_id | d1vfga2 |
| 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.218.1.4 — Poly A polymerase head domain-like |
| 结构域编号 domain_id | d1vfgb1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.173 — Poly A polymerase C-terminal region-like |
| 超家族 Superfamily superfamily | a.173.1 — Poly A polymerase C-terminal region-like |
| 家族 Family family | a.173.1.1 — Poly A polymerase C-terminal region-like |
| 结构域编号 domain_id | d1vfgb2 |
| 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.218.1.4 — Poly A polymerase head domain-like |
| 结构域编号 domain_id | d1vfgb3 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 1vfgA01 |
| 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 | 1vfgA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3090 — cca-adding enzyme, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — cca-adding enzyme, domain 2 |
| 结构域编号 domain_id | 1vfgB01 |
| 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 | 1vfgB02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3090 — cca-adding enzyme, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — cca-adding enzyme, domain 2 |