1ldj
Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase 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 | 1ldj |
| 沉积日期 deposition_date | 2002-04-08 |
| 结构标题 title | Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex |
| 关键词 keywords | cullin, rbx1, roc1, hrt1, zinc ring finger, ligase, ubiquitin, ubiquitination, SCF; LIGASE |
| 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 | 45.92 Å |
| 回转半径 Rg (电子) rg_electron | 46.94 Å |
| 零角强度 I(0) i0 | 134244000.00 |
| 分子量 molecular_weight | 95021.0 kDa |
| 排除体积 excluded_volume | 119090 ų |
| 包络体积 envelope_volume | 170890 ų |
| 水化壳体积 shell_volume | 33795 ų |
| 包络直径 envelope_diameter | 162.8 Å |
| 壳层 Rg shell_rg | 44.41 Å |
| 包络 Rg envelope_rg | 46.58 Å |
| 形状 Rg shape_rg | 46.98 Å |
| 总 Rg total_rg | 46.68 Å |
| 总原子数 total_atoms | 6668 |
| 残基数 n_residues | 813 |
| 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 | 150.6 Å |
| Rg (实空间) rg_real | 46.79 Å |
| Rg 误差 (实空间) rg_real_error | 1.90 Å |
| I(0) (实空间) i0_real | 1.3420e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.6580e+06 |
| Rg (倒空间) rg_reciprocal | 45.93 Å |
| I(0) (倒空间) i0_reciprocal | 134100000.0000 |
| 解质量估计 total_estimate | 0.4931 |
| 解质量评级 solution_quality | SUSPICIOUS a SUSPICIOUS solution |
| P(r) 峰数 n_peaks | 3 |
| 主峰位置 r_peak_primary | 31.0 Å |
| 偏度 Skewness skewness | 0.536 |
| 峰度 Kurtosis kurtosis | -0.690 |
| 角度范围 angular_range | — – 0.1700 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 5619000.0000 |
| 实空间数据点数 n_real_points | 35 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.537; Stabil: 0.999; Sysdev: 0.115; Positv: 1.000; Valcen: 0.436; Smooth: 0.014 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (3)
6. 折叠分类 (SCOP + CATH) 12 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1ldja1 |
| 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.4.5.34 — SCF ubiquitin ligase complex WHB domain |
| 结构域编号 domain_id | d1ldja2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.118 — alpha-alpha superhelix |
| 超家族 Superfamily superfamily | a.118.17 — Cullin repeat-like |
| 家族 Family family | a.118.17.1 — Cullin repeat |
| 结构域编号 domain_id | d1ldja3 |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.40 — Cullin homology domain |
| 超家族 Superfamily superfamily | e.40.1 — Cullin homology domain |
| 家族 Family family | e.40.1.1 — Cullin homology domain |
| 结构域编号 domain_id | d1ldjb_ |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.44 — RING/U-box |
| 超家族 Superfamily superfamily | g.44.1 — RING/U-box |
| 家族 Family family | g.44.1.1 — RING finger domain, C3HC4 |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 1ldjA01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1310 — 5 helical Cullin repeat like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cullin Repeats |
| 结构域编号 domain_id | 1ldjA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1310 — 5 helical Cullin repeat like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cullin Repeats |
| 结构域编号 domain_id | 1ldjA03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1310 — 5 helical Cullin repeat like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cullin Repeats |
| 结构域编号 domain_id | 1ldjA04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1310 — 5 helical Cullin repeat like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cullin Repeats |
| 结构域编号 domain_id | 1ldjA05 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 1030 — Ring Box Chain A; domain 5 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ring Box Chain A; domain 5 |
| 结构域编号 domain_id | 1ldjA06 |
| 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 |
| 结构域编号 domain_id | 1ldjA07 |
| 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 |
| 结构域编号 domain_id | 1ldjB00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 40 — Herpes Virus-1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Zinc/RING finger domain, C3HC4 (zinc finger) |