1go3
Structure of an archeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex
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 | 1go3 |
| 沉积日期 deposition_date | 2001-10-17 |
| 结构标题 title | Structure of an archeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex |
| 关键词 keywords | TRANSFERASE, TRANSFERASE; TRANSCRIPTION; DNA-DIRECTED RNA POLYMERASE; 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 | 42.11 Å |
| 回转半径 Rg (电子) rg_electron | 42.56 Å |
| 零角强度 I(0) i0 | 50129500.00 |
| 分子量 molecular_weight | 61918.0 kDa |
| 排除体积 excluded_volume | 79348 ų |
| 包络体积 envelope_volume | 110230 ų |
| 水化壳体积 shell_volume | 23677 ų |
| 包络直径 envelope_diameter | 147.7 Å |
| 壳层 Rg shell_rg | 42.99 Å |
| 包络 Rg envelope_rg | 41.36 Å |
| 形状 Rg shape_rg | 42.58 Å |
| 总 Rg total_rg | 42.50 Å |
| 总原子数 total_atoms | 4367 |
| 残基数 n_residues | 564 |
| 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 | 153.9 Å |
| Rg (实空间) rg_real | 42.73 Å |
| Rg 误差 (实空间) rg_real_error | 2.85 Å |
| I(0) (实空间) i0_real | 5.0130e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.0440e+06 |
| Rg (倒空间) rg_reciprocal | 42.12 Å |
| I(0) (倒空间) i0_reciprocal | 50090000.0000 |
| 解质量估计 total_estimate | 0.6410 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 25.0 Å |
| 偏度 Skewness skewness | 0.452 |
| 峰度 Kurtosis kurtosis | -0.841 |
| 角度范围 angular_range | — – 0.1850 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 3137000.0000 |
| 实空间数据点数 n_real_points | 38 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.112; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.056; Smooth: 0.936 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (3)
6. 折叠分类 (SCOP + CATH) 14 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1go3e1 |
| 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.40.4.5 — Cold shock DNA-binding domain-like |
| 结构域编号 domain_id | d1go3e2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.230 — Dodecin subunit-like |
| 超家族 Superfamily superfamily | d.230.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE) |
| 家族 Family family | d.230.1.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE) |
| 结构域编号 domain_id | d1go3f_ |
| 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.60.8.2 — RNA polymerase II subunit RBP4 (RpoF) |
| 结构域编号 domain_id | d1go3m1 |
| 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.40.4.5 — Cold shock DNA-binding domain-like |
| 结构域编号 domain_id | d1go3m2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.230 — Dodecin subunit-like |
| 超家族 Superfamily superfamily | d.230.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE) |
| 家族 Family family | d.230.1.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE) |
| 结构域编号 domain_id | d1go3n_ |
| 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.60.8.2 — RNA polymerase II subunit RBP4 (RpoF) |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 1go3E01 |
| 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 | 1go3E02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1490 — Dna Ligase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 120 — RNA polymerase Rpb7-like, N-terminal domain |
| 结构域编号 domain_id | 1go3F01 |
| 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 |
| 结构域编号 domain_id | 1go3F02 |
| 类 Class class | 6 — Special |
| 架构 Architecture architecture | 10 — Helix non-globular |
| 拓扑 Topology topology | 140 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 10 — |
| 结构域编号 domain_id | 1go3M01 |
| 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 | 1go3M02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1490 — Dna Ligase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 120 — RNA polymerase Rpb7-like, N-terminal domain |
| 结构域编号 domain_id | 1go3N01 |
| 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 |
| 结构域编号 domain_id | 1go3N02 |
| 类 Class class | 6 — Special |
| 架构 Architecture architecture | 10 — Helix non-globular |
| 拓扑 Topology topology | 140 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 10 — |