1l5j
CRYSTAL STRUCTURE OF E. COLI ACONITASE B.
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 | 1l5j |
| 沉积日期 deposition_date | 2002-03-07 |
| 结构标题 title | CRYSTAL STRUCTURE OF E. COLI ACONITASE B. |
| 关键词 keywords | Molecular recognition, RNA binding, Citric acid cycle, HEAT-like domain, 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 | 39.78 Å |
| 回转半径 Rg (电子) rg_electron | 39.83 Å |
| 零角强度 I(0) i0 | 518974000.00 |
| 分子量 molecular_weight | 187310.0 kDa |
| 排除体积 excluded_volume | 234720 ų |
| 包络体积 envelope_volume | 305180 ų |
| 水化壳体积 shell_volume | 62919 ų |
| 包络直径 envelope_diameter | 137.5 Å |
| 壳层 Rg shell_rg | 46.09 Å |
| 包络 Rg envelope_rg | 40.05 Å |
| 形状 Rg shape_rg | 39.86 Å |
| 总 Rg total_rg | 40.03 Å |
| 总原子数 total_atoms | 13142 |
| 残基数 n_residues | 1724 |
| 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 | 135.2 Å |
| Rg (实空间) rg_real | 39.92 Å |
| Rg 误差 (实空间) rg_real_error | 1.06 Å |
| I(0) (实空间) i0_real | 5.1900e+08 |
| I(0) 误差 (实空间) i0_real_error | 7.7020e+06 |
| Rg (倒空间) rg_reciprocal | 39.84 Å |
| I(0) (倒空间) i0_reciprocal | 518900000.0000 |
| 解质量估计 total_estimate | 0.8664 |
| 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 | 40.6 Å |
| 偏度 Skewness skewness | 0.436 |
| 峰度 Kurtosis kurtosis | -0.361 |
| 角度范围 angular_range | — – 0.2000 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 133000000.0000 |
| 实空间数据点数 n_real_points | 41 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.807; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.868 |
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) 16 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1l5ja1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.118 — alpha-alpha superhelix |
| 超家族 Superfamily superfamily | a.118.15 — Aconitase B, N-terminal domain |
| 家族 Family family | a.118.15.1 — Aconitase B, N-terminal domain |
| 结构域编号 domain_id | d1l5ja2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.8 — The 'swivelling' beta/beta/alpha domain |
| 超家族 Superfamily superfamily | c.8.2 — LeuD/IlvD-like |
| 家族 Family family | c.8.2.1 — LeuD-like |
| 结构域编号 domain_id | d1l5ja3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.83 — Aconitase iron-sulfur domain |
| 超家族 Superfamily superfamily | c.83.1 — Aconitase iron-sulfur domain |
| 家族 Family family | c.83.1.1 — Aconitase iron-sulfur domain |
| 结构域编号 domain_id | d1l5jb1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.118 — alpha-alpha superhelix |
| 超家族 Superfamily superfamily | a.118.15 — Aconitase B, N-terminal domain |
| 家族 Family family | a.118.15.1 — Aconitase B, N-terminal domain |
| 结构域编号 domain_id | d1l5jb2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.8 — The 'swivelling' beta/beta/alpha domain |
| 超家族 Superfamily superfamily | c.8.2 — LeuD/IlvD-like |
| 家族 Family family | c.8.2.1 — LeuD-like |
| 结构域编号 domain_id | d1l5jb3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.83 — Aconitase iron-sulfur domain |
| 超家族 Superfamily superfamily | c.83.1 — Aconitase iron-sulfur domain |
| 家族 Family family | c.83.1.1 — Aconitase iron-sulfur domain |
CATH v4.4 (10 domains)
| 结构域编号 domain_id | 1l5jA01 |
| 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 | 310 — Aconitate B, HEAT-like domain |
| 结构域编号 domain_id | 1l5jA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 19 — Aconitase; domain 4 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Aconitase, domain 4 |
| 结构域编号 domain_id | 1l5jA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1060 — Aconitase; Domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Aconitase, Domain 2 |
| 结构域编号 domain_id | 1l5jA04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 499 — Aconitase; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Aconitase, domain 3 |
| 结构域编号 domain_id | 1l5jA05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 499 — Aconitase; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Aconitase, domain 3 |
| 结构域编号 domain_id | 1l5jB01 |
| 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 | 310 — Aconitate B, HEAT-like domain |
| 结构域编号 domain_id | 1l5jB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 19 — Aconitase; domain 4 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Aconitase, domain 4 |
| 结构域编号 domain_id | 1l5jB03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1060 — Aconitase; Domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Aconitase, Domain 2 |
| 结构域编号 domain_id | 1l5jB04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 499 — Aconitase; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Aconitase, domain 3 |
| 结构域编号 domain_id | 1l5jB05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 499 — Aconitase; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Aconitase, domain 3 |