2jeb
Structure of a 9-subunit archaeal exosome bound to Mn ions
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 | 2jeb |
| 沉积日期 deposition_date | 2007-01-16 |
| 结构标题 title | Structure of a 9-subunit archaeal exosome bound to Mn ions |
| 关键词 keywords | ;NUCLEASE, HYDROLASE, RNA-BINDING, EXONUCLEASE, PHOSPHOROLYTIC, EXORIBONUCLEASE, RNA DEGRADATION, RNA, RRP4, RRP42, RRP41, EXOSOME, ARCHAEAL, RNASE PH ;; HYDROLASE |
| 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 | 29.63 Å |
| 回转半径 Rg (电子) rg_electron | 29.13 Å |
| 零角强度 I(0) i0 | 84024100.00 |
| 分子量 molecular_weight | 74737.0 kDa |
| 排除体积 excluded_volume | 94729 ų |
| 包络体积 envelope_volume | 119850 ų |
| 水化壳体积 shell_volume | 34988 ų |
| 包络直径 envelope_diameter | 105.5 Å |
| 壳层 Rg shell_rg | 35.71 Å |
| 包络 Rg envelope_rg | 29.28 Å |
| 形状 Rg shape_rg | 29.18 Å |
| 总 Rg total_rg | 29.64 Å |
| 总原子数 total_atoms | 5258 |
| 残基数 n_residues | 702 |
| 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 | 101.3 Å |
| Rg (实空间) rg_real | 29.67 Å |
| Rg 误差 (实空间) rg_real_error | 0.75 Å |
| I(0) (实空间) i0_real | 8.4020e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.2380e+06 |
| Rg (倒空间) rg_reciprocal | 29.66 Å |
| I(0) (倒空间) i0_reciprocal | 84020000.0000 |
| 解质量估计 total_estimate | 0.8793 |
| 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 | 32.5 Å |
| 偏度 Skewness skewness | 0.394 |
| 峰度 Kurtosis kurtosis | -0.299 |
| 角度范围 angular_range | — – 0.2650 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 14340000.0000 |
| 实空间数据点数 n_real_points | 54 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.983 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (7)
6. 折叠分类 (SCOP + CATH) 12 domains
SCOP 2.08 (7 domains)
| 结构域编号 domain_id | d2jeba1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.14 — Ribosomal protein S5 domain 2-like |
| 超家族 Superfamily superfamily | d.14.1 — Ribosomal protein S5 domain 2-like |
| 家族 Family family | d.14.1.4 — Ribonuclease PH domain 1-like |
| 结构域编号 domain_id | d2jeba2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.101 — Ribonuclease PH domain 2-like |
| 超家族 Superfamily superfamily | d.101.1 — Ribonuclease PH domain 2-like |
| 家族 Family family | d.101.1.1 — Ribonuclease PH domain 2-like |
| 结构域编号 domain_id | d2jeba3 |
| 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 |
| 结构域编号 domain_id | d2jebb1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.14 — Ribosomal protein S5 domain 2-like |
| 超家族 Superfamily superfamily | d.14.1 — Ribosomal protein S5 domain 2-like |
| 家族 Family family | d.14.1.4 — Ribonuclease PH domain 1-like |
| 结构域编号 domain_id | d2jebb2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.101 — Ribonuclease PH domain 2-like |
| 超家族 Superfamily superfamily | d.101.1 — Ribonuclease PH domain 2-like |
| 家族 Family family | d.101.1.1 — Ribonuclease PH domain 2-like |
| 结构域编号 domain_id | d2jebi1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.84 — Barrel-sandwich hybrid |
| 超家族 Superfamily superfamily | b.84.4 — Ribosomal L27 protein-like |
| 家族 Family family | b.84.4.0 — automated matches |
| 结构域编号 domain_id | d2jebi2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.40 — OB-fold |
| 超家族 Superfamily superfamily | b.40.4 — Nucleic acid-binding proteins |
| 家族 Family family | b.40.4.11 — DNA replication initiator (cdc21/cdc54) N-terminal domain |
CATH v4.4 (5 domains)
| 结构域编号 domain_id | 2jebA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 230 — Ribosomal Protein S5; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 70 — GHMP Kinase, N-terminal domain |
| 结构域编号 domain_id | 2jebB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 230 — Ribosomal Protein S5; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 70 — GHMP Kinase, N-terminal domain |
| 结构域编号 domain_id | 2jebI01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P) |
| 同源超家族 H-superfamily homologous superfamily | 100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain |
| 结构域编号 domain_id | 2jebI02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P) |
| 同源超家族 H-superfamily homologous superfamily | 140 — Nucleic acid-binding proteins |
| 结构域编号 domain_id | 2jebI03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1370 — Ribosomal Protein S8; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — K Homology domain, type 1 |