1miy
Crystal structure of Bacillus stearothermophilus CCA-adding enzyme in complex with CTP
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 | 1miy |
| 沉积日期 deposition_date | 2002-08-23 |
| 结构标题 title | Crystal structure of Bacillus stearothermophilus CCA-adding enzyme in complex with CTP |
| 关键词 keywords | CCA-adding enzyme, tRNA nucleotidyltransferase, TRANSLATION, TRANSFERASE; TRANSLATION, TRANSFERASE |
| 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 | 35.37 Å |
| 回转半径 Rg (电子) rg_electron | 35.17 Å |
| 零角强度 I(0) i0 | 124537000.00 |
| 分子量 molecular_weight | 89328.0 kDa |
| 排除体积 excluded_volume | 112170 ų |
| 包络体积 envelope_volume | 159510 ų |
| 水化壳体积 shell_volume | 40052 ų |
| 包络直径 envelope_diameter | 143.4 Å |
| 壳层 Rg shell_rg | 39.09 Å |
| 包络 Rg envelope_rg | 35.32 Å |
| 形状 Rg shape_rg | 35.20 Å |
| 总 Rg total_rg | 35.36 Å |
| 总原子数 total_atoms | 6286 |
| 残基数 n_residues | 790 |
| 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 | 135.2 Å |
| Rg (实空间) rg_real | 35.58 Å |
| Rg 误差 (实空间) rg_real_error | 1.53 Å |
| I(0) (实空间) i0_real | 1.2450e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.2840e+06 |
| Rg (倒空间) rg_reciprocal | 35.45 Å |
| I(0) (倒空间) i0_reciprocal | 124500000.0000 |
| 解质量估计 total_estimate | 0.8211 |
| 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 | 42.0 Å |
| 偏度 Skewness skewness | 0.544 |
| 峰度 Kurtosis kurtosis | 0.209 |
| 角度范围 angular_range | — – 0.2250 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 10860000.0000 |
| 实空间数据点数 n_real_points | 46 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.628; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.814; Smooth: 0.973 |
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) 12 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1miya1 |
| 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 | d1miya2 |
| 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 | d1miyb1 |
| 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 | d1miyb2 |
| 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 |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 1miyA01 |
| 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 | 1miyA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 110 — Hydrophobic Seed Protein |
| 同源超家族 H-superfamily homologous superfamily | 30 — |
| 结构域编号 domain_id | 1miyA03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 560 — |
| 结构域编号 domain_id | 1miyA04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 246 — Serum Albumin; Chain A, Domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 80 — |
| 结构域编号 domain_id | 1miyB01 |
| 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 | 1miyB02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 110 — Hydrophobic Seed Protein |
| 同源超家族 H-superfamily homologous superfamily | 30 — |
| 结构域编号 domain_id | 1miyB03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 560 — |
| 结构域编号 domain_id | 1miyB04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 246 — Serum Albumin; Chain A, Domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 80 — |