2io2
Crystal structure of human Senp2 in complex with RanGAP1-SUMO-1
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 | 2io2 |
| 沉积日期 deposition_date | 2006-10-09 |
| 结构标题 title | Crystal structure of human Senp2 in complex with RanGAP1-SUMO-1 |
| 关键词 keywords | SUMO, Ubiquitin, Senp, Ulp, complex, PROTEIN BINDING, HYDROLASE; PROTEIN BINDING, HYDROLASE |
| 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 | 26.54 Å |
| 回转半径 Rg (电子) rg_electron | 25.76 Å |
| 零角强度 I(0) i0 | 43547100.00 |
| 分子量 molecular_weight | 52409.0 kDa |
| 排除体积 excluded_volume | 66284 ų |
| 包络体积 envelope_volume | 86893 ų |
| 水化壳体积 shell_volume | 28449 ų |
| 包络直径 envelope_diameter | 88.1 Å |
| 壳层 Rg shell_rg | 32.75 Å |
| 包络 Rg envelope_rg | 25.99 Å |
| 形状 Rg shape_rg | 25.73 Å |
| 总 Rg total_rg | 26.68 Å |
| 总原子数 total_atoms | 3688 |
| 残基数 n_residues | 456 |
| 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 | 83.6 Å |
| Rg (实空间) rg_real | 26.48 Å |
| Rg 误差 (实空间) rg_real_error | 0.44 Å |
| I(0) (实空间) i0_real | 4.3550e+07 |
| I(0) 误差 (实空间) i0_real_error | 5.6020e+05 |
| Rg (倒空间) rg_reciprocal | 26.50 Å |
| I(0) (倒空间) i0_reciprocal | 43550000.0000 |
| 解质量估计 total_estimate | 0.9106 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 30.6 Å |
| 偏度 Skewness skewness | 0.231 |
| 峰度 Kurtosis kurtosis | -0.532 |
| 角度范围 angular_range | — – 0.3000 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 6296000.0000 |
| 实空间数据点数 n_real_points | 61 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.990 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (4)
6. 折叠分类 (SCOP + CATH) 6 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d2io2a_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.3 — Cysteine proteinases |
| 超家族 Superfamily superfamily | d.3.1 — Cysteine proteinases |
| 家族 Family family | d.3.1.7 — Adenain-like |
| 结构域编号 domain_id | d2io2b_ |
| 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 | d2io2c1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.118 — alpha-alpha superhelix |
| 超家族 Superfamily superfamily | a.118.12 — Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain |
| 家族 Family family | a.118.12.1 — Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain |
CATH v4.4 (3 domains)
| 结构域编号 domain_id | 2io2A00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 395 — Adenoviral Proteinase; Chain |
| 同源超家族 H-superfamily homologous superfamily | 10 — Adenoviral Proteinase; Chain A |
| 结构域编号 domain_id | 2io2B00 |
| 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 | 2io2C00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 25 — Alpha Horseshoe |
| 拓扑 Topology topology | 40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat |
| 同源超家族 H-superfamily homologous superfamily | 200 — Ran-GTPase activating protein 1, C-terminal domain |