1y0v
Crystal structure of anthrax edema factor (EF) in complex with calmodulin and pyrophosphate
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 | 1y0v |
| 沉积日期 deposition_date | 2004-11-16 |
| 结构标题 title | Crystal structure of anthrax edema factor (EF) in complex with calmodulin and pyrophosphate |
| 关键词 keywords | Calcium-Independent, Calmodulin, Anthrax edema factor, LYASE; LYASE |
| 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 | 81.07 Å |
| 回转半径 Rg (电子) rg_electron | 80.88 Å |
| 零角强度 I(0) i0 | 5026280000.00 |
| 分子量 molecular_weight | 608970.0 kDa |
| 排除体积 excluded_volume | 764760 ų |
| 包络体积 envelope_volume | 1440800 ų |
| 水化壳体积 shell_volume | 151280 ų |
| 包络直径 envelope_diameter | 273.2 Å |
| 壳层 Rg shell_rg | 78.82 Å |
| 包络 Rg envelope_rg | 75.89 Å |
| 形状 Rg shape_rg | 80.89 Å |
| 总 Rg total_rg | 80.83 Å |
| 总原子数 total_atoms | 42906 |
| 残基数 n_residues | 5286 |
| 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 | 285.7 Å |
| Rg (实空间) rg_real | 81.53 Å |
| Rg 误差 (实空间) rg_real_error | 2.25 Å |
| I(0) (实空间) i0_real | 5.0320e+09 |
| I(0) 误差 (实空间) i0_real_error | 1.1160e+08 |
| Rg (倒空间) rg_reciprocal | 81.68 Å |
| I(0) (倒空间) i0_reciprocal | 5035000000.0000 |
| 解质量估计 total_estimate | 0.8563 |
| 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 | 105.3 Å |
| 偏度 Skewness skewness | 0.215 |
| 峰度 Kurtosis kurtosis | -0.226 |
| 角度范围 angular_range | — – 0.0950 Å−1 |
| 当前正则化参数 α current_alpha | 0.1420 |
| 最高正则化参数 α highest_alpha | 198400000.0000 |
| 实空间数据点数 n_real_points | 20 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.801; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.745 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (5)
6. 折叠分类 (SCOP + CATH) 42 domains
SCOP 2.08 (12 domains)
| 结构域编号 domain_id | d1y0vh1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.39 — EF Hand-like |
| 超家族 Superfamily superfamily | a.39.1 — EF-hand |
| 家族 Family family | a.39.1.5 — Calmodulin-like |
| 结构域编号 domain_id | d1y0vh2 |
| 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 | d1y0vi1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.39 — EF Hand-like |
| 超家族 Superfamily superfamily | a.39.1 — EF-hand |
| 家族 Family family | a.39.1.5 — Calmodulin-like |
| 结构域编号 domain_id | d1y0vi2 |
| 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 | d1y0vj1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.39 — EF Hand-like |
| 超家族 Superfamily superfamily | a.39.1 — EF-hand |
| 家族 Family family | a.39.1.5 — Calmodulin-like |
| 结构域编号 domain_id | d1y0vj2 |
| 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 | d1y0vk1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.39 — EF Hand-like |
| 超家族 Superfamily superfamily | a.39.1 — EF-hand |
| 家族 Family family | a.39.1.5 — Calmodulin-like |
| 结构域编号 domain_id | d1y0vk2 |
| 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 | d1y0vl1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.39 — EF Hand-like |
| 超家族 Superfamily superfamily | a.39.1 — EF-hand |
| 家族 Family family | a.39.1.5 — Calmodulin-like |
| 结构域编号 domain_id | d1y0vl2 |
| 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 | d1y0vm1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.39 — EF Hand-like |
| 超家族 Superfamily superfamily | a.39.1 — EF-hand |
| 家族 Family family | a.39.1.5 — Calmodulin-like |
| 结构域编号 domain_id | d1y0vm2 |
| 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 |
CATH v4.4 (30 domains)
| 结构域编号 domain_id | 1y0vA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 390 — Collagenase (Catalytic Domain) |
| 同源超家族 H-superfamily homologous superfamily | 10 — Collagenase (Catalytic Domain) |
| 结构域编号 domain_id | 1y0vA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1760 — Adenylylcyclase toxin fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — Anthrax toxin, edema factor, central domain |
| 结构域编号 domain_id | 1y0vA04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 60 — |
| 结构域编号 domain_id | 1y0vB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 390 — Collagenase (Catalytic Domain) |
| 同源超家族 H-superfamily homologous superfamily | 10 — Collagenase (Catalytic Domain) |
| 结构域编号 domain_id | 1y0vB03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1760 — Adenylylcyclase toxin fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — Anthrax toxin, edema factor, central domain |
| 结构域编号 domain_id | 1y0vB04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 60 — |
| 结构域编号 domain_id | 1y0vC01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 390 — Collagenase (Catalytic Domain) |
| 同源超家族 H-superfamily homologous superfamily | 10 — Collagenase (Catalytic Domain) |
| 结构域编号 domain_id | 1y0vC03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1760 — Adenylylcyclase toxin fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — Anthrax toxin, edema factor, central domain |
| 结构域编号 domain_id | 1y0vC04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 60 — |
| 结构域编号 domain_id | 1y0vD01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 390 — Collagenase (Catalytic Domain) |
| 同源超家族 H-superfamily homologous superfamily | 10 — Collagenase (Catalytic Domain) |
| 结构域编号 domain_id | 1y0vD03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1760 — Adenylylcyclase toxin fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — Anthrax toxin, edema factor, central domain |
| 结构域编号 domain_id | 1y0vD04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 60 — |
| 结构域编号 domain_id | 1y0vE01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 390 — Collagenase (Catalytic Domain) |
| 同源超家族 H-superfamily homologous superfamily | 10 — Collagenase (Catalytic Domain) |
| 结构域编号 domain_id | 1y0vE03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1760 — Adenylylcyclase toxin fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — Anthrax toxin, edema factor, central domain |
| 结构域编号 domain_id | 1y0vE04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 60 — |
| 结构域编号 domain_id | 1y0vF01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 390 — Collagenase (Catalytic Domain) |
| 同源超家族 H-superfamily homologous superfamily | 10 — Collagenase (Catalytic Domain) |
| 结构域编号 domain_id | 1y0vF03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1760 — Adenylylcyclase toxin fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — Anthrax toxin, edema factor, central domain |
| 结构域编号 domain_id | 1y0vF04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 60 — |
| 结构域编号 domain_id | 1y0vH01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 238 — Recoverin; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — EF-hand |
| 结构域编号 domain_id | 1y0vH02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 238 — Recoverin; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — EF-hand |
| 结构域编号 domain_id | 1y0vI01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 238 — Recoverin; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — EF-hand |
| 结构域编号 domain_id | 1y0vI02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 238 — Recoverin; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — EF-hand |
| 结构域编号 domain_id | 1y0vJ01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 238 — Recoverin; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — EF-hand |
| 结构域编号 domain_id | 1y0vJ02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 238 — Recoverin; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — EF-hand |
| 结构域编号 domain_id | 1y0vK01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 238 — Recoverin; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — EF-hand |
| 结构域编号 domain_id | 1y0vK02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 238 — Recoverin; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — EF-hand |
| 结构域编号 domain_id | 1y0vL01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 238 — Recoverin; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — EF-hand |
| 结构域编号 domain_id | 1y0vL02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 238 — Recoverin; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — EF-hand |
| 结构域编号 domain_id | 1y0vM01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 238 — Recoverin; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — EF-hand |
| 结构域编号 domain_id | 1y0vM02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 238 — Recoverin; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — EF-hand |