1kps
Structural Basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin conjugating enzyme Ubc9 and RanGAP1
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 | 1kps |
| 沉积日期 deposition_date | 2002-01-02 |
| 结构标题 title | Structural Basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin conjugating enzyme Ubc9 and RanGAP1 |
| 关键词 keywords | SUMO, UBIQUITIN, E2, CONJUGATING ENZYME, LIGASE, THIOESTER, SMALL UBIQUITIN-LIKE MODIFIER, LIGASE-PROTEIN TRANSPORT COMPLEX; LIGASE/PROTEIN TRANSPORT |
| 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 | 31.21 Å |
| 回转半径 Rg (电子) rg_electron | 30.47 Å |
| 零角强度 I(0) i0 | 74282200.00 |
| 分子量 molecular_weight | 70425.0 kDa |
| 排除体积 excluded_volume | 89301 ų |
| 包络体积 envelope_volume | 114040 ų |
| 水化壳体积 shell_volume | 32108 ų |
| 包络直径 envelope_diameter | 110.1 Å |
| 壳层 Rg shell_rg | 36.61 Å |
| 包络 Rg envelope_rg | 30.49 Å |
| 形状 Rg shape_rg | 30.44 Å |
| 总 Rg total_rg | 31.17 Å |
| 总原子数 total_atoms | 4952 |
| 残基数 n_residues | 626 |
| 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 | 103.4 Å |
| Rg (实空间) rg_real | 31.17 Å |
| Rg 误差 (实空间) rg_real_error | 0.71 Å |
| I(0) (实空间) i0_real | 7.4280e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.1430e+06 |
| Rg (倒空间) rg_reciprocal | 31.19 Å |
| I(0) (倒空间) i0_reciprocal | 74280000.0000 |
| 解质量估计 total_estimate | 0.8947 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 42.6 Å |
| 偏度 Skewness skewness | 0.220 |
| 峰度 Kurtosis kurtosis | -0.543 |
| 角度范围 angular_range | — – 0.2550 Å−1 |
| 当前正则化参数 α current_alpha | 0.0001 |
| 最高正则化参数 α highest_alpha | 18430000.0000 |
| 实空间数据点数 n_real_points | 52 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.987 |
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) 9 domains
SCOP 2.08 (5 domains)
| 结构域编号 domain_id | d1kpsa1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.20 — UBC-like |
| 超家族 Superfamily superfamily | d.20.1 — UBC-like |
| 家族 Family family | d.20.1.1 — UBC-related |
| 结构域编号 domain_id | d1kpsa2 |
| 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 | d1kpsb_ |
| 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 |
| 结构域编号 domain_id | d1kpsc_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.20 — UBC-like |
| 超家族 Superfamily superfamily | d.20.1 — UBC-like |
| 家族 Family family | d.20.1.1 — UBC-related |
| 结构域编号 domain_id | d1kpsd_ |
| 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 (4 domains)
| 结构域编号 domain_id | 1kpsA00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 110 — Ubiquitin Conjugating Enzyme |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ubiquitin Conjugating Enzyme |
| 结构域编号 domain_id | 1kpsB00 |
| 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 |
| 结构域编号 domain_id | 1kpsC00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 110 — Ubiquitin Conjugating Enzyme |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ubiquitin Conjugating Enzyme |
| 结构域编号 domain_id | 1kpsD00 |
| 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 |