2ivd
Structure of protoporphyrinogen oxidase from Myxococcus xanthus with acifluorfen
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 | 2ivd |
| 沉积日期 deposition_date | 2006-06-12 |
| 结构标题 title | Structure of protoporphyrinogen oxidase from Myxococcus xanthus with acifluorfen |
| 关键词 keywords | ;PROTOPORPHYRINOGEN OXIDASE, PORPHYRIN BIOSYNTHESIS, CHLOROPHYLL BIOSYNTHESIS, OXIDOREDUCTASE, HAEM BIOSYNTHESIS, HEME BIOSYNTHESIS, FAD, PORPHYRIA, ACIFLUORFEN, FLAVOPROTEIN ;; 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 | 38.41 Å |
| 回转半径 Rg (电子) rg_electron | 38.20 Å |
| 零角强度 I(0) i0 | 148257000.00 |
| 分子量 molecular_weight | 97087.0 kDa |
| 排除体积 excluded_volume | 121310 ų |
| 包络体积 envelope_volume | 167770 ų |
| 水化壳体积 shell_volume | 38409 ų |
| 包络直径 envelope_diameter | 137.1 Å |
| 壳层 Rg shell_rg | 42.34 Å |
| 包络 Rg envelope_rg | 37.00 Å |
| 形状 Rg shape_rg | 38.21 Å |
| 总 Rg total_rg | 38.45 Å |
| 总原子数 total_atoms | 6841 |
| 残基数 n_residues | 898 |
| 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 | 131.7 Å |
| Rg (实空间) rg_real | 38.74 Å |
| Rg 误差 (实空间) rg_real_error | 1.47 Å |
| I(0) (实空间) i0_real | 1.4830e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.6460e+06 |
| Rg (倒空间) rg_reciprocal | 38.54 Å |
| I(0) (倒空间) i0_reciprocal | 148200000.0000 |
| 解质量估计 total_estimate | 0.8249 |
| 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 | 32.1 Å |
| 偏度 Skewness skewness | 0.427 |
| 峰度 Kurtosis kurtosis | -0.528 |
| 角度范围 angular_range | — – 0.2050 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 20090000.0000 |
| 实空间数据点数 n_real_points | 42 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.737; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.765; Smooth: 0.743 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (6)
6. 折叠分类 (SCOP + CATH) 10 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d2ivda1 |
| 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 | d2ivda2 |
| 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 | d2ivdb1 |
| 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 | d2ivdb2 |
| 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 | 2ivdA01 |
| 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 | 2ivdA02 |
| 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 | 2ivdA03 |
| 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 | 2ivdB01 |
| 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 | 2ivdB02 |
| 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 | 2ivdB03 |
| 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 |