1muu
2.0 A crystal structure of GDP-mannose dehydrogenase
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 | 1muu |
| 沉积日期 deposition_date | 2002-09-24 |
| 结构标题 title | 2.0 A crystal structure of GDP-mannose dehydrogenase |
| 关键词 keywords | Rossmann fold; domain-swapped dimer; enzyme complex with cofactor and product, 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 | 37.13 Å |
| 回转半径 Rg (电子) rg_electron | 36.35 Å |
| 零角强度 I(0) i0 | 575480000.00 |
| 分子量 molecular_weight | 189700.0 kDa |
| 排除体积 excluded_volume | 234480 ų |
| 包络体积 envelope_volume | 286190 ų |
| 水化壳体积 shell_volume | 63061 ų |
| 包络直径 envelope_diameter | 115.8 Å |
| 壳层 Rg shell_rg | 44.53 Å |
| 包络 Rg envelope_rg | 36.03 Å |
| 形状 Rg shape_rg | 36.43 Å |
| 总 Rg total_rg | 36.55 Å |
| 总原子数 total_atoms | 13179 |
| 残基数 n_residues | 1708 |
| 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 | 112.3 Å |
| Rg (实空间) rg_real | 36.86 Å |
| Rg 误差 (实空间) rg_real_error | 0.70 Å |
| I(0) (实空间) i0_real | 5.7550e+08 |
| I(0) 误差 (实空间) i0_real_error | 8.3880e+06 |
| Rg (倒空间) rg_reciprocal | 37.03 Å |
| I(0) (倒空间) i0_reciprocal | 575600000.0000 |
| 解质量估计 total_estimate | 0.8324 |
| 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 | 49.6 Å |
| 偏度 Skewness skewness | 0.054 |
| 峰度 Kurtosis kurtosis | -0.573 |
| 角度范围 angular_range | — – 0.2150 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 135400000.0000 |
| 实空间数据点数 n_real_points | 44 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.000 |
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) 24 domains
SCOP 2.08 (12 domains)
| 结构域编号 domain_id | d1muua1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like |
| 超家族 Superfamily superfamily | a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like |
| 家族 Family family | a.100.1.4 — UDP-glucose/GDP-mannose dehydrogenase dimerisation domain |
| 结构域编号 domain_id | d1muua2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.2 — NAD(P)-binding Rossmann-fold domains |
| 超家族 Superfamily superfamily | c.2.1 — NAD(P)-binding Rossmann-fold domains |
| 家族 Family family | c.2.1.6 — 6-phosphogluconate dehydrogenase-like, N-terminal domain |
| 结构域编号 domain_id | d1muua3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.26 — Adenine nucleotide alpha hydrolase-like |
| 超家族 Superfamily superfamily | c.26.3 — UDP-glucose/GDP-mannose dehydrogenase C-terminal domain |
| 家族 Family family | c.26.3.1 — UDP-glucose/GDP-mannose dehydrogenase C-terminal domain |
| 结构域编号 domain_id | d1muub1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like |
| 超家族 Superfamily superfamily | a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like |
| 家族 Family family | a.100.1.4 — UDP-glucose/GDP-mannose dehydrogenase dimerisation domain |
| 结构域编号 domain_id | d1muub2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.2 — NAD(P)-binding Rossmann-fold domains |
| 超家族 Superfamily superfamily | c.2.1 — NAD(P)-binding Rossmann-fold domains |
| 家族 Family family | c.2.1.6 — 6-phosphogluconate dehydrogenase-like, N-terminal domain |
| 结构域编号 domain_id | d1muub3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.26 — Adenine nucleotide alpha hydrolase-like |
| 超家族 Superfamily superfamily | c.26.3 — UDP-glucose/GDP-mannose dehydrogenase C-terminal domain |
| 家族 Family family | c.26.3.1 — UDP-glucose/GDP-mannose dehydrogenase C-terminal domain |
| 结构域编号 domain_id | d1muuc1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like |
| 超家族 Superfamily superfamily | a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like |
| 家族 Family family | a.100.1.4 — UDP-glucose/GDP-mannose dehydrogenase dimerisation domain |
| 结构域编号 domain_id | d1muuc2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.2 — NAD(P)-binding Rossmann-fold domains |
| 超家族 Superfamily superfamily | c.2.1 — NAD(P)-binding Rossmann-fold domains |
| 家族 Family family | c.2.1.6 — 6-phosphogluconate dehydrogenase-like, N-terminal domain |
| 结构域编号 domain_id | d1muuc3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.26 — Adenine nucleotide alpha hydrolase-like |
| 超家族 Superfamily superfamily | c.26.3 — UDP-glucose/GDP-mannose dehydrogenase C-terminal domain |
| 家族 Family family | c.26.3.1 — UDP-glucose/GDP-mannose dehydrogenase C-terminal domain |
| 结构域编号 domain_id | d1muud1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like |
| 超家族 Superfamily superfamily | a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like |
| 家族 Family family | a.100.1.4 — UDP-glucose/GDP-mannose dehydrogenase dimerisation domain |
| 结构域编号 domain_id | d1muud2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.2 — NAD(P)-binding Rossmann-fold domains |
| 超家族 Superfamily superfamily | c.2.1 — NAD(P)-binding Rossmann-fold domains |
| 家族 Family family | c.2.1.6 — 6-phosphogluconate dehydrogenase-like, N-terminal domain |
| 结构域编号 domain_id | d1muud3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.26 — Adenine nucleotide alpha hydrolase-like |
| 超家族 Superfamily superfamily | c.26.3 — UDP-glucose/GDP-mannose dehydrogenase C-terminal domain |
| 家族 Family family | c.26.3.1 — UDP-glucose/GDP-mannose dehydrogenase C-terminal domain |
CATH v4.4 (12 domains)
| 结构域编号 domain_id | 1muuA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1muuA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 170 — |
| 结构域编号 domain_id | 1muuA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1muuB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1muuB02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 170 — |
| 结构域编号 domain_id | 1muuB03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1muuC01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1muuC02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 170 — |
| 结构域编号 domain_id | 1muuC03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1muuD01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1muuD02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 170 — |
| 结构域编号 domain_id | 1muuD03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 720 — NAD(P)-binding Rossmann-like Domain |