2hbm
;Structure of the yeast nuclear exosome component, Rrp6p, reveals an interplay between the active site and the HRDC domain; Protein in complex with Mn, Zn, and UMP ;
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 | 2hbm |
| 沉积日期 deposition_date | 2006-06-14 |
| 结构标题 title | ;Structure of the yeast nuclear exosome component, Rrp6p, reveals an interplay between the active site and the HRDC domain; Protein in complex with Mn, Zn, and UMP ; |
| 关键词 keywords | exosome, RNA metabolism, RNA surveillance, RNA processing, HYDROLASE, GENE REGULATION; HYDROLASE, GENE REGULATION |
| 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 | 24.32 Å |
| 回转半径 Rg (电子) rg_electron | 23.61 Å |
| 零角强度 I(0) i0 | 34559000.00 |
| 分子量 molecular_weight | 45952.0 kDa |
| 排除体积 excluded_volume | 57759 ų |
| 包络体积 envelope_volume | 69539 ų |
| 水化壳体积 shell_volume | 25039 ų |
| 包络直径 envelope_diameter | 87.3 Å |
| 壳层 Rg shell_rg | 30.11 Å |
| 包络 Rg envelope_rg | 23.98 Å |
| 形状 Rg shape_rg | 23.59 Å |
| 总 Rg total_rg | 24.44 Å |
| 总原子数 total_atoms | 3239 |
| 残基数 n_residues | 390 |
| 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 | 85.1 Å |
| Rg (实空间) rg_real | 24.38 Å |
| Rg 误差 (实空间) rg_real_error | 0.62 Å |
| I(0) (实空间) i0_real | 3.4560e+07 |
| I(0) 误差 (实空间) i0_real_error | 4.8310e+05 |
| Rg (倒空间) rg_reciprocal | 24.37 Å |
| I(0) (倒空间) i0_reciprocal | 34560000.0000 |
| 解质量估计 total_estimate | 0.6868 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 27.0 Å |
| 偏度 Skewness skewness | 0.456 |
| 峰度 Kurtosis kurtosis | -0.167 |
| 角度范围 angular_range | — – 0.3250 Å−1 |
| 当前正则化参数 α current_alpha | 0.0001 |
| 最高正则化参数 α highest_alpha | 9503000.0000 |
| 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: 0.749; Stabil: 1.000; Sysdev: 0.264; Positv: 1.000; Valcen: 0.890; Smooth: 0.995 |
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) 5 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d2hbma1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.60 — SAM domain-like |
| 超家族 Superfamily superfamily | a.60.8 — HRDC-like |
| 家族 Family family | a.60.8.4 — EXOSC10 HRDC domain-like |
| 结构域编号 domain_id | d2hbma2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.55 — Ribonuclease H-like motif |
| 超家族 Superfamily superfamily | c.55.3 — Ribonuclease H-like |
| 家族 Family family | c.55.3.5 — DnaQ-like 3'-5' exonuclease |
| 结构域编号 domain_id | d2hbma3 |
| 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 (2 domains)
| 结构域编号 domain_id | 2hbmA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 420 — Nucleotidyltransferase; domain 5 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ribonuclease H-like superfamily/Ribonuclease H |
| 结构域编号 domain_id | 2hbmA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 150 — DNA polymerase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 80 — HRDC domain |