2iuk
Crystal structure of Soybean Lipoxygenase-D
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 | 2iuk |
| 沉积日期 deposition_date | 2006-06-05 |
| 结构标题 title | Crystal structure of Soybean Lipoxygenase-D |
| 关键词 keywords | ;IRON, DIOXYGENASE, METAL-BINDING, OXIDOREDUCTASE, OXYLIPIN BIOSYNTHESIS, SOYBEAN LIPOXYGENASE-D, FATTY ACID BIOSYNTHESIS, LIPID SYNTHESIS ;; OXIDOREDUCTASE |
| 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 | 54.88 Å |
| 回转半径 Rg (电子) rg_electron | 55.59 Å |
| 零角强度 I(0) i0 | 476026000.00 |
| 分子量 molecular_weight | 188180.0 kDa |
| 排除体积 excluded_volume | 237770 ų |
| 包络体积 envelope_volume | 310670 ų |
| 水化壳体积 shell_volume | 49035 ų |
| 包络直径 envelope_diameter | 189.9 Å |
| 壳层 Rg shell_rg | 52.16 Å |
| 包络 Rg envelope_rg | 55.11 Å |
| 形状 Rg shape_rg | 55.55 Å |
| 总 Rg total_rg | 55.62 Å |
| 总原子数 total_atoms | 13298 |
| 残基数 n_residues | 1668 |
| 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 | 175.4 Å |
| Rg (实空间) rg_real | 55.54 Å |
| Rg 误差 (实空间) rg_real_error | 2.36 Å |
| I(0) (实空间) i0_real | 4.7600e+08 |
| I(0) 误差 (实空间) i0_real_error | 9.7930e+06 |
| Rg (倒空间) rg_reciprocal | 54.27 Å |
| I(0) (倒空间) i0_reciprocal | 475100000.0000 |
| 解质量估计 total_estimate | 0.6367 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 3 |
| 主峰位置 r_peak_primary | 36.3 Å |
| 偏度 Skewness skewness | 0.439 |
| 峰度 Kurtosis kurtosis | -0.897 |
| 角度范围 angular_range | — – 0.1450 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 70000000.0000 |
| 实空间数据点数 n_real_points | 30 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.283; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.398; Smooth: 0.025 |
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) 14 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d2iuka1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.12 — Lipase/lipooxygenase domain (PLAT/LH2 domain) |
| 超家族 Superfamily superfamily | b.12.1 — Lipase/lipooxygenase domain (PLAT/LH2 domain) |
| 家族 Family family | b.12.1.0 — automated matches |
| 结构域编号 domain_id | d2iuka2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.119 — Lipoxigenase |
| 超家族 Superfamily superfamily | a.119.1 — Lipoxigenase |
| 家族 Family family | a.119.1.1 — Plant lipoxigenases |
| 结构域编号 domain_id | d2iukb1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.12 — Lipase/lipooxygenase domain (PLAT/LH2 domain) |
| 超家族 Superfamily superfamily | b.12.1 — Lipase/lipooxygenase domain (PLAT/LH2 domain) |
| 家族 Family family | b.12.1.0 — automated matches |
| 结构域编号 domain_id | d2iukb2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.119 — Lipoxigenase |
| 超家族 Superfamily superfamily | a.119.1 — Lipoxigenase |
| 家族 Family family | a.119.1.1 — Plant lipoxigenases |
CATH v4.4 (10 domains)
| 结构域编号 domain_id | 2iukA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 60 — Lipoxygenase-1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — PLAT/LH2 domain |
| 结构域编号 domain_id | 2iukA02 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 375 — Lipoxygenase-1; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Lipoxygenase-1; Domain 2 |
| 结构域编号 domain_id | 2iukA03 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 372 — Lipoxygenase-1; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Lipoxygenase-1; Domain 3 |
| 结构域编号 domain_id | 2iukA04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 450 — Nuclear Transport Factor 2; Chain: A, |
| 同源超家族 H-superfamily homologous superfamily | 60 — |
| 结构域编号 domain_id | 2iukA05 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 245 — Lipoxygenase-1; domain 5 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Lipoxygenase-1; Domain 5 |
| 结构域编号 domain_id | 2iukB01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 60 — Lipoxygenase-1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — PLAT/LH2 domain |
| 结构域编号 domain_id | 2iukB02 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 375 — Lipoxygenase-1; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Lipoxygenase-1; Domain 2 |
| 结构域编号 domain_id | 2iukB03 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 372 — Lipoxygenase-1; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Lipoxygenase-1; Domain 3 |
| 结构域编号 domain_id | 2iukB04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 450 — Nuclear Transport Factor 2; Chain: A, |
| 同源超家族 H-superfamily homologous superfamily | 60 — |
| 结构域编号 domain_id | 2iukB05 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 245 — Lipoxygenase-1; domain 5 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Lipoxygenase-1; Domain 5 |