1yx5
Solution Structure of S5a UIM-1/Ubiquitin 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 | 1yx5 |
| 沉积日期 deposition_date | 2005-02-19 |
| 结构标题 title | Solution Structure of S5a UIM-1/Ubiquitin Complex |
| 关键词 keywords | polyubiquitin, proteasome, S5a, UIM, HYDROLASE; HYDROLASE |
| 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 | 35.91 Å |
| 回转半径 Rg (电子) rg_electron | 36.01 Å |
| 零角强度 I(0) i0 | 2092760000.00 |
| 分子量 molecular_weight | 368820.0 kDa |
| 排除体积 excluded_volume | 454840 ų |
| 包络体积 envelope_volume | 293800 ų |
| 水化壳体积 shell_volume | 52004 ų |
| 包络直径 envelope_diameter | 152.8 Å |
| 壳层 Rg shell_rg | 49.39 Å |
| 包络 Rg envelope_rg | 48.91 Å |
| 形状 Rg shape_rg | 36.00 Å |
| 总 Rg total_rg | 36.32 Å |
| 总原子数 total_atoms | 51246 |
| 残基数 n_residues | 3384 |
| 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 | 139.7 Å |
| Rg (实空间) rg_real | 36.62 Å |
| Rg 误差 (实空间) rg_real_error | 2.01 Å |
| I(0) (实空间) i0_real | 2.0930e+09 |
| I(0) 误差 (实空间) i0_real_error | 3.9570e+07 |
| Rg (倒空间) rg_reciprocal | 36.19 Å |
| I(0) (倒空间) i0_reciprocal | 2092000000.0000 |
| 解质量估计 total_estimate | 0.6259 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 3 |
| 主峰位置 r_peak_primary | 19.1 Å |
| 偏度 Skewness skewness | 0.502 |
| 峰度 Kurtosis kurtosis | -0.692 |
| 角度范围 angular_range | — – 0.2200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 1133000.0000 |
| 实空间数据点数 n_real_points | 45 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.043; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.009; Smooth: 0.995 |
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) 4 domains
SCOP 2.08 (1 domains)
| 结构域编号 domain_id | d1yx5b_ |
| 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.15.1.0 — automated matches |
CATH v4.4 (3 domains)
| 结构域编号 domain_id | 1yx5A01 |
| 类 Class class | 6 — Special |
| 架构 Architecture architecture | 10 — Helix non-globular |
| 拓扑 Topology topology | 250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 380 — |
| 结构域编号 domain_id | 1yx5A02 |
| 类 Class class | 6 — Special |
| 架构 Architecture architecture | 10 — Helix non-globular |
| 拓扑 Topology topology | 300 — cAMP-dependent Protein Kinase, Chain A |
| 同源超家族 H-superfamily homologous superfamily | 40 — |
| 结构域编号 domain_id | 1yx5B00 |
| 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 |