2jy6
Solution structure of the complex of ubiquitin and ubiquilin 1 UBA domain
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 | 2jy6 |
| 沉积日期 deposition_date | 2007-12-06 |
| 结构标题 title | Solution structure of the complex of ubiquitin and ubiquilin 1 UBA domain |
| 关键词 keywords | Ubiquilin, UBA, Ubiquitin, complex, Alternative splicing, Cytoplasm, Nucleus, Phosphoprotein, Proteasome, SIGNALING PROTEIN; SIGNALING PROTEIN |
| 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 | 16.20 Å |
| 回转半径 Rg (电子) rg_electron | 15.76 Å |
| 零角强度 I(0) i0 | 290015000.00 |
| 分子量 molecular_weight | 141930.0 kDa |
| 排除体积 excluded_volume | 177590 ų |
| 包络体积 envelope_volume | 27753 ų |
| 水化壳体积 shell_volume | 14429 ų |
| 包络直径 envelope_diameter | 58.6 Å |
| 壳层 Rg shell_rg | 22.28 Å |
| 包络 Rg envelope_rg | 17.23 Å |
| 形状 Rg shape_rg | 15.77 Å |
| 总 Rg total_rg | 15.92 Å |
| 总原子数 total_atoms | 20160 |
| 残基数 n_residues | 1280 |
| 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 | 55.1 Å |
| Rg (实空间) rg_real | 16.25 Å |
| Rg 误差 (实空间) rg_real_error | 0.31 Å |
| I(0) (实空间) i0_real | 2.9000e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.2500e+06 |
| Rg (倒空间) rg_reciprocal | 16.25 Å |
| I(0) (倒空间) i0_reciprocal | 290000000.0000 |
| 解质量估计 total_estimate | 0.8495 |
| 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 | 16.9 Å |
| 偏度 Skewness skewness | 0.420 |
| 峰度 Kurtosis kurtosis | -0.187 |
| 角度范围 angular_range | — – 0.4900 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 520600.0000 |
| 实空间数据点数 n_real_points | 79 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.702; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.957 |
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
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d2jy6a_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.15 — beta-Grasp (ubiquitin-like) |
| 超家族 Superfamily superfamily | d.15.1 — Ubiquitin-like |
| 家族 Family family | d.15.1.1 — Ubiquitin-related |
| 结构域编号 domain_id | d2jy6b1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.5 — RuvA C-terminal domain-like |
| 超家族 Superfamily superfamily | a.5.2 — UBA-like |
| 家族 Family family | a.5.2.1 — UBA domain |
| 结构域编号 domain_id | d2jy6b2 |
| 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 | d2jy6b3 |
| 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 | 2jy6A00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 20 — Ubiquitin-like (UB roll) |
| 同源超家族 H-superfamily homologous superfamily | 90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 |
| 结构域编号 domain_id | 2jy6B00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 8 — Helicase, Ruva Protein; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ubiquitin-associated (UBA) domain |