1sez
Crystal Structure of Protoporphyrinogen IX Oxidase
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 | 1sez |
| 沉积日期 deposition_date | 2004-02-19 |
| 结构标题 title | Crystal Structure of Protoporphyrinogen IX Oxidase |
| 关键词 keywords | FAD-binding, Para-hydroxy-benzoate-hydroxylase fold (PHBH-fold), monotopic membrane-binding domain, OXIDOREDUCTASE; 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 | 37.36 Å |
| 回转半径 Rg (电子) rg_electron | 36.83 Å |
| 零角强度 I(0) i0 | 164826000.00 |
| 分子量 molecular_weight | 102580.0 kDa |
| 排除体积 excluded_volume | 127440 ų |
| 包络体积 envelope_volume | 171870 ų |
| 水化壳体积 shell_volume | 39659 ų |
| 包络直径 envelope_diameter | 123.5 Å |
| 壳层 Rg shell_rg | 42.51 Å |
| 包络 Rg envelope_rg | 35.85 Å |
| 形状 Rg shape_rg | 36.85 Å |
| 总 Rg total_rg | 37.16 Å |
| 总原子数 total_atoms | 7152 |
| 残基数 n_residues | 912 |
| 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 | 119.4 Å |
| Rg (实空间) rg_real | 37.43 Å |
| Rg 误差 (实空间) rg_real_error | 0.99 Å |
| I(0) (实空间) i0_real | 1.6480e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.0100e+06 |
| Rg (倒空间) rg_reciprocal | 37.40 Å |
| I(0) (倒空间) i0_reciprocal | 164800000.0000 |
| 解质量估计 total_estimate | 0.8691 |
| 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 | 31.3 Å |
| 偏度 Skewness skewness | 0.213 |
| 峰度 Kurtosis kurtosis | -0.860 |
| 角度范围 angular_range | — – 0.2100 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 22620000.0000 |
| 实空间数据点数 n_real_points | 43 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.919; Smooth: 0.846 |
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) 10 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1seza1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.3 — FAD/NAD(P)-binding domain |
| 超家族 Superfamily superfamily | c.3.1 — FAD/NAD(P)-binding domain |
| 家族 Family family | c.3.1.2 — FAD-linked reductases, N-terminal domain |
| 结构域编号 domain_id | d1seza2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.16 — FAD-linked reductases, C-terminal domain |
| 超家族 Superfamily superfamily | d.16.1 — FAD-linked reductases, C-terminal domain |
| 家族 Family family | d.16.1.5 — L-aminoacid/polyamine oxidase |
| 结构域编号 domain_id | d1sezb1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.3 — FAD/NAD(P)-binding domain |
| 超家族 Superfamily superfamily | c.3.1 — FAD/NAD(P)-binding domain |
| 家族 Family family | c.3.1.2 — FAD-linked reductases, N-terminal domain |
| 结构域编号 domain_id | d1sezb2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.16 — FAD-linked reductases, C-terminal domain |
| 超家族 Superfamily superfamily | d.16.1 — FAD-linked reductases, C-terminal domain |
| 家族 Family family | d.16.1.5 — L-aminoacid/polyamine oxidase |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1sezA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 50 — FAD/NAD(P)-binding domain |
| 同源超家族 H-superfamily homologous superfamily | 60 — FAD/NAD(P)-binding domain |
| 结构域编号 domain_id | 1sezA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 660 — Polyamine Oxidase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Protoporphyrinogen oxidase, mitochondrial; domain 2 |
| 结构域编号 domain_id | 1sezA03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3110 — protoporphyrinogen ix oxidase, domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — protoporphyrinogen ix oxidase, domain 3 |
| 结构域编号 domain_id | 1sezB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 50 — FAD/NAD(P)-binding domain |
| 同源超家族 H-superfamily homologous superfamily | 60 — FAD/NAD(P)-binding domain |
| 结构域编号 domain_id | 1sezB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 660 — Polyamine Oxidase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Protoporphyrinogen oxidase, mitochondrial; domain 2 |
| 结构域编号 domain_id | 1sezB03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3110 — protoporphyrinogen ix oxidase, domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — protoporphyrinogen ix oxidase, domain 3 |