2b3j
Crystal Structure of Staphylococcus aureus tRNA Adenosine Deaminase, TadA, in Complex with RNA
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 | 2b3j |
| 沉积日期 deposition_date | 2005-09-20 |
| 结构标题 title | Crystal Structure of Staphylococcus aureus tRNA Adenosine Deaminase, TadA, in Complex with RNA |
| 关键词 keywords | mixed alpha-beta, protein-rna complex, RNA stem-loop, HYDROLASE-RNA COMPLEX; HYDROLASE/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 | 28.22 Å |
| 回转半径 Rg (电子) rg_electron | 27.56 Å |
| 零角强度 I(0) i0 | 145502000.00 |
| 分子量 molecular_weight | 82497.0 kDa |
| 排除体积 excluded_volume | 97715 ų |
| 包络体积 envelope_volume | 118970 ų |
| 水化壳体积 shell_volume | 35429 ų |
| 包络直径 envelope_diameter | 94.5 Å |
| 壳层 Rg shell_rg | 35.21 Å |
| 包络 Rg envelope_rg | 27.47 Å |
| 形状 Rg shape_rg | 27.60 Å |
| 总 Rg total_rg | 28.09 Å |
| 总原子数 total_atoms | 5691 |
| 残基数 n_residues | 654 |
| 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 | 91.0 Å |
| Rg (实空间) rg_real | 28.09 Å |
| Rg 误差 (实空间) rg_real_error | 0.52 Å |
| I(0) (实空间) i0_real | 1.4550e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.1740e+06 |
| Rg (倒空间) rg_reciprocal | 28.13 Å |
| I(0) (倒空间) i0_reciprocal | 145500000.0000 |
| 解质量估计 total_estimate | 0.9019 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 35.8 Å |
| 偏度 Skewness skewness | 0.189 |
| 峰度 Kurtosis kurtosis | -0.488 |
| 角度范围 angular_range | — – 0.2800 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 20220000.0000 |
| 实空间数据点数 n_real_points | 57 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.993 |
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) 8 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d2b3ja1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.97 — Cytidine deaminase-like |
| 超家族 Superfamily superfamily | c.97.1 — Cytidine deaminase-like |
| 家族 Family family | c.97.1.2 — Deoxycytidylate deaminase-like |
| 结构域编号 domain_id | d2b3jb_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.97 — Cytidine deaminase-like |
| 超家族 Superfamily superfamily | c.97.1 — Cytidine deaminase-like |
| 家族 Family family | c.97.1.2 — Deoxycytidylate deaminase-like |
| 结构域编号 domain_id | d2b3jc_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.97 — Cytidine deaminase-like |
| 超家族 Superfamily superfamily | c.97.1 — Cytidine deaminase-like |
| 家族 Family family | c.97.1.2 — Deoxycytidylate deaminase-like |
| 结构域编号 domain_id | d2b3jd_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.97 — Cytidine deaminase-like |
| 超家族 Superfamily superfamily | c.97.1 — Cytidine deaminase-like |
| 家族 Family family | c.97.1.2 — Deoxycytidylate deaminase-like |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 2b3jA00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 140 — Cytidine Deaminase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cytidine Deaminase, domain 2 |
| 结构域编号 domain_id | 2b3jB00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 140 — Cytidine Deaminase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cytidine Deaminase, domain 2 |
| 结构域编号 domain_id | 2b3jC00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 140 — Cytidine Deaminase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cytidine Deaminase, domain 2 |
| 结构域编号 domain_id | 2b3jD00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 140 — Cytidine Deaminase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cytidine Deaminase, domain 2 |