2d0v
Crystal structure of methanol dehydrogenase from Hyphomicrobium denitrificans
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 | 2d0v |
| 沉积日期 deposition_date | 2005-08-09 |
| 结构标题 title | Crystal structure of methanol dehydrogenase from Hyphomicrobium denitrificans |
| 关键词 keywords | electron transfer, oxidoreductase, calcium binding, methanol, PQQ; 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 | 46.64 Å |
| 回转半径 Rg (电子) rg_electron | 47.06 Å |
| 零角强度 I(0) i0 | 752674000.00 |
| 分子量 molecular_weight | 223180.0 kDa |
| 排除体积 excluded_volume | 276850 ų |
| 包络体积 envelope_volume | 337670 ų |
| 水化壳体积 shell_volume | 63126 ų |
| 包络直径 envelope_diameter | 160.9 Å |
| 壳层 Rg shell_rg | 47.58 Å |
| 包络 Rg envelope_rg | 46.87 Å |
| 形状 Rg shape_rg | 47.03 Å |
| 总 Rg total_rg | 47.16 Å |
| 总原子数 total_atoms | 15764 |
| 残基数 n_residues | 1997 |
| 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 | 165.7 Å |
| Rg (实空间) rg_real | 47.15 Å |
| Rg 误差 (实空间) rg_real_error | 2.06 Å |
| I(0) (实空间) i0_real | 7.5270e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.4620e+07 |
| Rg (倒空间) rg_reciprocal | 46.64 Å |
| I(0) (倒空间) i0_reciprocal | 752200000.0000 |
| 解质量估计 total_estimate | 0.8077 |
| 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 | 39.0 Å |
| 偏度 Skewness skewness | 0.516 |
| 峰度 Kurtosis kurtosis | -0.470 |
| 角度范围 angular_range | — – 0.1700 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 305100000.0000 |
| 实空间数据点数 n_real_points | 35 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.634; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.788; Smooth: 0.807 |
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) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d2d0va_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.70 — 8-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.70.1 — Quinoprotein alcohol dehydrogenase-like |
| 家族 Family family | b.70.1.1 — Quinoprotein alcohol dehydrogenase-like |
| 结构域编号 domain_id | d2d0vb_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.137 — Non-globular all-alpha subunits of globular proteins |
| 超家族 Superfamily superfamily | a.137.2 — Methanol dehydrogenase subunit |
| 家族 Family family | a.137.2.1 — Methanol dehydrogenase subunit |
| 结构域编号 domain_id | d2d0vd_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.70 — 8-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.70.1 — Quinoprotein alcohol dehydrogenase-like |
| 家族 Family family | b.70.1.1 — Quinoprotein alcohol dehydrogenase-like |
| 结构域编号 domain_id | d2d0ve_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.137 — Non-globular all-alpha subunits of globular proteins |
| 超家族 Superfamily superfamily | a.137.2 — Methanol dehydrogenase subunit |
| 家族 Family family | a.137.2.1 — Methanol dehydrogenase subunit |
| 结构域编号 domain_id | d2d0vi_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.70 — 8-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.70.1 — Quinoprotein alcohol dehydrogenase-like |
| 家族 Family family | b.70.1.1 — Quinoprotein alcohol dehydrogenase-like |
| 结构域编号 domain_id | d2d0vj_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.137 — Non-globular all-alpha subunits of globular proteins |
| 超家族 Superfamily superfamily | a.137.2 — Methanol dehydrogenase subunit |
| 家族 Family family | a.137.2.1 — Methanol dehydrogenase subunit |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 2d0vA00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 140 — 8 Propeller |
| 拓扑 Topology topology | 10 — Methanol Dehydrogenase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Quinoprotein alcohol dehydrogenase-like superfamily |
| 结构域编号 domain_id | 2d0vB00 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 160 — Methanol Dehydrogenase; Chain B |
| 同源超家族 H-superfamily homologous superfamily | 10 — Methanol dehydrogenase, beta subunit |
| 结构域编号 domain_id | 2d0vD00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 140 — 8 Propeller |
| 拓扑 Topology topology | 10 — Methanol Dehydrogenase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Quinoprotein alcohol dehydrogenase-like superfamily |
| 结构域编号 domain_id | 2d0vE00 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 160 — Methanol Dehydrogenase; Chain B |
| 同源超家族 H-superfamily homologous superfamily | 10 — Methanol dehydrogenase, beta subunit |
| 结构域编号 domain_id | 2d0vI00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 140 — 8 Propeller |
| 拓扑 Topology topology | 10 — Methanol Dehydrogenase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Quinoprotein alcohol dehydrogenase-like superfamily |
| 结构域编号 domain_id | 2d0vJ00 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 160 — Methanol Dehydrogenase; Chain B |
| 同源超家族 H-superfamily homologous superfamily | 10 — Methanol dehydrogenase, beta subunit |