2ckz
X-ray structure of RNA polymerase III subcomplex C17-C25.
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 | 2ckz |
| 沉积日期 deposition_date | 2006-04-24 |
| 结构标题 title | X-ray structure of RNA polymerase III subcomplex C17-C25. |
| 关键词 keywords | ;DNA-DIRECTED RNA POLYMERASE, MULTIPROTEIN COMPLEX, NUCLEOTIDYLTRANSFERASE, NUCLEAR PROTEIN, HYPOTHETICAL PROTEIN, EUKARYOTIC NUCLEIC ACID POLYMERASE, CLASS III GENE TRANSCRIPTION, TRANSFERASE, TRANSCRIPTION, TRNA SYNTHESIS ;; 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 | 35.23 Å |
| 回转半径 Rg (电子) rg_electron | 35.46 Å |
| 零角强度 I(0) i0 | 55459600.00 |
| 分子量 molecular_weight | 62155.0 kDa |
| 排除体积 excluded_volume | 79046 ų |
| 包络体积 envelope_volume | 105940 ų |
| 水化壳体积 shell_volume | 29003 ų |
| 包络直径 envelope_diameter | 135.5 Å |
| 壳层 Rg shell_rg | 35.72 Å |
| 包络 Rg envelope_rg | 35.31 Å |
| 形状 Rg shape_rg | 35.45 Å |
| 总 Rg total_rg | 35.51 Å |
| 总原子数 total_atoms | 4386 |
| 残基数 n_residues | 541 |
| 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 | 125.2 Å |
| Rg (实空间) rg_real | 35.79 Å |
| Rg 误差 (实空间) rg_real_error | 1.35 Å |
| I(0) (实空间) i0_real | 5.5460e+07 |
| I(0) 误差 (实空间) i0_real_error | 9.3620e+05 |
| Rg (倒空间) rg_reciprocal | 35.44 Å |
| I(0) (倒空间) i0_reciprocal | 55440000.0000 |
| 解质量估计 total_estimate | 0.7452 |
| 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 | 27.8 Å |
| 偏度 Skewness skewness | 0.644 |
| 峰度 Kurtosis kurtosis | -0.234 |
| 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 | 8816000.0000 |
| 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: 0.556; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.392; Smooth: 0.623 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (2)
6. 折叠分类 (SCOP + CATH) 6 domains
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 2ckzA01 |
| 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 | 870 — |
| 结构域编号 domain_id | 2ckzB01 |
| 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 | 2ckzB02 |
| 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 | 2ckzC01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1250 — Growth Hormone; Chain: A; |
| 同源超家族 H-superfamily homologous superfamily | 40 — RNA Polymerase II, Rpb4 subunit |
| 结构域编号 domain_id | 2ckzD01 |
| 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 | 2ckzD02 |
| 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 |