2dym
The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-46) 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 | 2dym |
| 沉积日期 deposition_date | 2006-09-15 |
| 结构标题 title | The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-46) complex |
| 关键词 keywords | ubiquitin-fold, herix-bundle, PROTEIN TURNOVER-PROTEIN TURNOVER COMPLEX; PROTEIN TURNOVER/PROTEIN TURNOVER |
| 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 | 40.04 Å |
| 回转半径 Rg (电子) rg_electron | 39.29 Å |
| 零角强度 I(0) i0 | 214060000.00 |
| 分子量 molecular_weight | 125620.0 kDa |
| 排除体积 excluded_volume | 159900 ų |
| 包络体积 envelope_volume | 216180 ų |
| 水化壳体积 shell_volume | 46195 ų |
| 包络直径 envelope_diameter | 132.7 Å |
| 壳层 Rg shell_rg | 44.73 Å |
| 包络 Rg envelope_rg | 38.07 Å |
| 形状 Rg shape_rg | 39.23 Å |
| 总 Rg total_rg | 39.87 Å |
| 总原子数 total_atoms | 8875 |
| 残基数 n_residues | 1109 |
| 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 | 122.3 Å |
| Rg (实空间) rg_real | 39.91 Å |
| Rg 误差 (实空间) rg_real_error | 1.00 Å |
| I(0) (实空间) i0_real | 2.1410e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.5770e+06 |
| Rg (倒空间) rg_reciprocal | 40.04 Å |
| I(0) (倒空间) i0_reciprocal | 214100000.0000 |
| 解质量估计 total_estimate | 0.8894 |
| 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 | 59.6 Å |
| 偏度 Skewness skewness | 0.045 |
| 峰度 Kurtosis kurtosis | -0.687 |
| 角度范围 angular_range | — – 0.1950 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 46600000.0000 |
| 实空间数据点数 n_real_points | 40 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.824 |
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
CATH v4.4 (12 domains)
| 结构域编号 domain_id | 2dymA01 |
| 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 | 620 — |
| 结构域编号 domain_id | 2dymA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 246 — Serum Albumin; Chain A, Domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 190 — Autophagy protein Apg5, helix rich domain |
| 结构域编号 domain_id | 2dymA03 |
| 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 | 2dymC01 |
| 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 | 620 — |
| 结构域编号 domain_id | 2dymC02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 246 — Serum Albumin; Chain A, Domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 190 — Autophagy protein Apg5, helix rich domain |
| 结构域编号 domain_id | 2dymC03 |
| 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 | 2dymE01 |
| 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 | 620 — |
| 结构域编号 domain_id | 2dymE02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 246 — Serum Albumin; Chain A, Domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 190 — Autophagy protein Apg5, helix rich domain |
| 结构域编号 domain_id | 2dymE03 |
| 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 | 2dymG01 |
| 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 | 620 — |
| 结构域编号 domain_id | 2dymG02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 246 — Serum Albumin; Chain A, Domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 190 — Autophagy protein Apg5, helix rich domain |
| 结构域编号 domain_id | 2dymG03 |
| 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 |