2f2h
Structure of the YicI thiosugar Michaelis complex
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 | 2f2h |
| 沉积日期 deposition_date | 2005-11-16 |
| 结构标题 title | Structure of the YicI thiosugar Michaelis complex |
| 关键词 keywords | beta8alpha8 barrel, HYDROLASE; HYDROLASE |
| 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 | 55.04 Å |
| 回转半径 Rg (电子) rg_electron | 54.45 Å |
| 零角强度 I(0) i0 | 4112840000.00 |
| 分子量 molecular_weight | 535530.0 kDa |
| 排除体积 excluded_volume | 666530 ų |
| 包络体积 envelope_volume | 857900 ų |
| 水化壳体积 shell_volume | 127070 ų |
| 包络直径 envelope_diameter | 178.6 Å |
| 壳层 Rg shell_rg | 61.27 Å |
| 包络 Rg envelope_rg | 53.43 Å |
| 形状 Rg shape_rg | 54.39 Å |
| 总 Rg total_rg | 54.81 Å |
| 总原子数 total_atoms | 37796 |
| 残基数 n_residues | 4638 |
| 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 | 178.9 Å |
| Rg (实空间) rg_real | 54.83 Å |
| Rg 误差 (实空间) rg_real_error | 1.40 Å |
| I(0) (实空间) i0_real | 4.1130e+09 |
| I(0) 误差 (实空间) i0_real_error | 7.7010e+07 |
| Rg (倒空间) rg_reciprocal | 55.20 Å |
| I(0) (倒空间) i0_reciprocal | 4115000000.0000 |
| 解质量估计 total_estimate | 0.8847 |
| 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 | 67.8 Å |
| 偏度 Skewness skewness | 0.161 |
| 峰度 Kurtosis kurtosis | -0.496 |
| 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 | 401500000.0000 |
| 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: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.834 |
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) 54 domains
SCOP 2.08 (30 domains)
| 结构域编号 domain_id | d2f2ha1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.150 — Glycolsyl hydrolase family 31 C-terminal domain-like |
| 超家族 Superfamily superfamily | b.150.1 — Glycolsyl hydrolase family 31 C-terminal domain |
| 家族 Family family | b.150.1.1 — Glycolsyl hydrolase family 31 C-terminal domain |
| 结构域编号 domain_id | d2f2ha2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.30 — Supersandwich |
| 超家族 Superfamily superfamily | b.30.5 — Galactose mutarotase-like |
| 家族 Family family | b.30.5.11 — Glycosyl hydrolase family 31, N-terminal domain-like |
| 结构域编号 domain_id | d2f2ha3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.71 — Glycosyl hydrolase domain |
| 超家族 Superfamily superfamily | b.71.1 — Glycosyl hydrolase domain |
| 家族 Family family | b.71.1.4 — Glycosyl hydrolase family 31, domain 3 |
| 结构域编号 domain_id | d2f2ha4 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.8 — (Trans)glycosidases |
| 家族 Family family | c.1.8.13 — Glycosyl hydrolase family 31 catalytic domain |
| 结构域编号 domain_id | d2f2ha5 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d2f2hb1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.150 — Glycolsyl hydrolase family 31 C-terminal domain-like |
| 超家族 Superfamily superfamily | b.150.1 — Glycolsyl hydrolase family 31 C-terminal domain |
| 家族 Family family | b.150.1.1 — Glycolsyl hydrolase family 31 C-terminal domain |
| 结构域编号 domain_id | d2f2hb2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.30 — Supersandwich |
| 超家族 Superfamily superfamily | b.30.5 — Galactose mutarotase-like |
| 家族 Family family | b.30.5.11 — Glycosyl hydrolase family 31, N-terminal domain-like |
| 结构域编号 domain_id | d2f2hb3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.71 — Glycosyl hydrolase domain |
| 超家族 Superfamily superfamily | b.71.1 — Glycosyl hydrolase domain |
| 家族 Family family | b.71.1.4 — Glycosyl hydrolase family 31, domain 3 |
| 结构域编号 domain_id | d2f2hb4 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.8 — (Trans)glycosidases |
| 家族 Family family | c.1.8.13 — Glycosyl hydrolase family 31 catalytic domain |
| 结构域编号 domain_id | d2f2hb5 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d2f2hc1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.150 — Glycolsyl hydrolase family 31 C-terminal domain-like |
| 超家族 Superfamily superfamily | b.150.1 — Glycolsyl hydrolase family 31 C-terminal domain |
| 家族 Family family | b.150.1.1 — Glycolsyl hydrolase family 31 C-terminal domain |
| 结构域编号 domain_id | d2f2hc2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.30 — Supersandwich |
| 超家族 Superfamily superfamily | b.30.5 — Galactose mutarotase-like |
| 家族 Family family | b.30.5.11 — Glycosyl hydrolase family 31, N-terminal domain-like |
| 结构域编号 domain_id | d2f2hc3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.71 — Glycosyl hydrolase domain |
| 超家族 Superfamily superfamily | b.71.1 — Glycosyl hydrolase domain |
| 家族 Family family | b.71.1.4 — Glycosyl hydrolase family 31, domain 3 |
| 结构域编号 domain_id | d2f2hc4 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.8 — (Trans)glycosidases |
| 家族 Family family | c.1.8.13 — Glycosyl hydrolase family 31 catalytic domain |
| 结构域编号 domain_id | d2f2hc5 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d2f2hd1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.150 — Glycolsyl hydrolase family 31 C-terminal domain-like |
| 超家族 Superfamily superfamily | b.150.1 — Glycolsyl hydrolase family 31 C-terminal domain |
| 家族 Family family | b.150.1.1 — Glycolsyl hydrolase family 31 C-terminal domain |
| 结构域编号 domain_id | d2f2hd2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.30 — Supersandwich |
| 超家族 Superfamily superfamily | b.30.5 — Galactose mutarotase-like |
| 家族 Family family | b.30.5.11 — Glycosyl hydrolase family 31, N-terminal domain-like |
| 结构域编号 domain_id | d2f2hd3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.71 — Glycosyl hydrolase domain |
| 超家族 Superfamily superfamily | b.71.1 — Glycosyl hydrolase domain |
| 家族 Family family | b.71.1.4 — Glycosyl hydrolase family 31, domain 3 |
| 结构域编号 domain_id | d2f2hd4 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.8 — (Trans)glycosidases |
| 家族 Family family | c.1.8.13 — Glycosyl hydrolase family 31 catalytic domain |
| 结构域编号 domain_id | d2f2hd5 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d2f2he1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.150 — Glycolsyl hydrolase family 31 C-terminal domain-like |
| 超家族 Superfamily superfamily | b.150.1 — Glycolsyl hydrolase family 31 C-terminal domain |
| 家族 Family family | b.150.1.1 — Glycolsyl hydrolase family 31 C-terminal domain |
| 结构域编号 domain_id | d2f2he2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.30 — Supersandwich |
| 超家族 Superfamily superfamily | b.30.5 — Galactose mutarotase-like |
| 家族 Family family | b.30.5.11 — Glycosyl hydrolase family 31, N-terminal domain-like |
| 结构域编号 domain_id | d2f2he3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.71 — Glycosyl hydrolase domain |
| 超家族 Superfamily superfamily | b.71.1 — Glycosyl hydrolase domain |
| 家族 Family family | b.71.1.4 — Glycosyl hydrolase family 31, domain 3 |
| 结构域编号 domain_id | d2f2he4 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.8 — (Trans)glycosidases |
| 家族 Family family | c.1.8.13 — Glycosyl hydrolase family 31 catalytic domain |
| 结构域编号 domain_id | d2f2he5 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d2f2hf1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.150 — Glycolsyl hydrolase family 31 C-terminal domain-like |
| 超家族 Superfamily superfamily | b.150.1 — Glycolsyl hydrolase family 31 C-terminal domain |
| 家族 Family family | b.150.1.1 — Glycolsyl hydrolase family 31 C-terminal domain |
| 结构域编号 domain_id | d2f2hf2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.30 — Supersandwich |
| 超家族 Superfamily superfamily | b.30.5 — Galactose mutarotase-like |
| 家族 Family family | b.30.5.11 — Glycosyl hydrolase family 31, N-terminal domain-like |
| 结构域编号 domain_id | d2f2hf3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.71 — Glycosyl hydrolase domain |
| 超家族 Superfamily superfamily | b.71.1 — Glycosyl hydrolase domain |
| 家族 Family family | b.71.1.4 — Glycosyl hydrolase family 31, domain 3 |
| 结构域编号 domain_id | d2f2hf4 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.8 — (Trans)glycosidases |
| 家族 Family family | c.1.8.13 — Glycosyl hydrolase family 31 catalytic domain |
| 结构域编号 domain_id | d2f2hf5 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
CATH v4.4 (24 domains)
| 结构域编号 domain_id | 2f2hA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1760 — glycosyl hydrolase (family 31) |
| 结构域编号 domain_id | 2f2hA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 80 — Glycosidases |
| 结构域编号 domain_id | 2f2hA03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1180 — Golgi alpha-mannosidase II |
| 结构域编号 domain_id | 2f2hA04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1180 — Golgi alpha-mannosidase II |
| 结构域编号 domain_id | 2f2hB01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1760 — glycosyl hydrolase (family 31) |
| 结构域编号 domain_id | 2f2hB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 80 — Glycosidases |
| 结构域编号 domain_id | 2f2hB03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1180 — Golgi alpha-mannosidase II |
| 结构域编号 domain_id | 2f2hB04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1180 — Golgi alpha-mannosidase II |
| 结构域编号 domain_id | 2f2hC01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1760 — glycosyl hydrolase (family 31) |
| 结构域编号 domain_id | 2f2hC02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 80 — Glycosidases |
| 结构域编号 domain_id | 2f2hC03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1180 — Golgi alpha-mannosidase II |
| 结构域编号 domain_id | 2f2hC04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1180 — Golgi alpha-mannosidase II |
| 结构域编号 domain_id | 2f2hD01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1760 — glycosyl hydrolase (family 31) |
| 结构域编号 domain_id | 2f2hD02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 80 — Glycosidases |
| 结构域编号 domain_id | 2f2hD03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1180 — Golgi alpha-mannosidase II |
| 结构域编号 domain_id | 2f2hD04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1180 — Golgi alpha-mannosidase II |
| 结构域编号 domain_id | 2f2hE01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1760 — glycosyl hydrolase (family 31) |
| 结构域编号 domain_id | 2f2hE02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 80 — Glycosidases |
| 结构域编号 domain_id | 2f2hE03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1180 — Golgi alpha-mannosidase II |
| 结构域编号 domain_id | 2f2hE04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1180 — Golgi alpha-mannosidase II |
| 结构域编号 domain_id | 2f2hF01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1760 — glycosyl hydrolase (family 31) |
| 结构域编号 domain_id | 2f2hF02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 80 — Glycosidases |
| 结构域编号 domain_id | 2f2hF03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1180 — Golgi alpha-mannosidase II |
| 结构域编号 domain_id | 2f2hF04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1180 — Golgi alpha-mannosidase II |