2dk5
Solution structure of Winged-Helix domain in RNA polymerase III 39KDa polypeptide
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 | 2dk5 |
| 沉积日期 deposition_date | 2006-04-06 |
| 结构标题 title | Solution structure of Winged-Helix domain in RNA polymerase III 39KDa polypeptide |
| 关键词 keywords | ;structural genomics, Winged helix domain, DNA-directed RNA polymerase III, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, TRANSLATION, TRANSFERASE ;; TRANSLATION, TRANSFERASE |
| 实验方法 method | SOLUTION NMR |
2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)
| 回转半径 Rg (Guinier) rg_guinier | 16.96 Å |
| 回转半径 Rg (电子) rg_electron | 15.95 Å |
| 零角强度 I(0) i0 | 546786000.00 |
| 分子量 molecular_weight | 196810.0 kDa |
| 排除体积 excluded_volume | 247320 ų |
| 包络体积 envelope_volume | 59429 ų |
| 水化壳体积 shell_volume | 20407 ų |
| 包络直径 envelope_diameter | 85.1 Å |
| 壳层 Rg shell_rg | 30.95 Å |
| 包络 Rg envelope_rg | 29.04 Å |
| 形状 Rg shape_rg | 15.93 Å |
| 总 Rg total_rg | 16.51 Å |
| 总原子数 total_atoms | 28200 |
| 残基数 n_residues | 1820 |
| 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 | 47.0 Å |
| Rg (实空间) rg_real | 15.38 Å |
| Rg 误差 (实空间) rg_real_error | 0.11 Å |
| I(0) (实空间) i0_real | 5.1950e+08 |
| I(0) 误差 (实空间) i0_real_error | 4.7760e+06 |
| Rg (倒空间) rg_reciprocal | 17.42 Å |
| I(0) (倒空间) i0_reciprocal | 546800000.0000 |
| 解质量估计 total_estimate | 0.6484 |
| 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 | 16.1 Å |
| 偏度 Skewness skewness | 0.573 |
| 峰度 Kurtosis kurtosis | -0.105 |
| 角度范围 angular_range | — – 0.4700 Å−1 |
| 当前正则化参数 α current_alpha | 1.9750 |
| 最高正则化参数 α highest_alpha | 345700.0000 |
| 实空间数据点数 n_real_points | 77 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.019; Oscil: 0.834; Stabil: 0.994; Sysdev: 0.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (1)
6. 折叠分类 (SCOP + CATH) 4 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d2dk5a1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.4 — DNA/RNA-binding 3-helical bundle |
| 超家族 Superfamily superfamily | a.4.5 — 'Winged helix' DNA-binding domain |
| 家族 Family family | a.4.5.85 — RPO3F domain-like |
| 结构域编号 domain_id | d2dk5a2 |
| 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 | d2dk5a3 |
| 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 (1 domains)
| 结构域编号 domain_id | 2dk5A01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain |