1uyp
The three-dimensional structure of beta-fructosidase (invertase) from Thermotoga maritima
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 | 1uyp |
| 沉积日期 deposition_date | 2004-03-02 |
| 结构标题 title | The three-dimensional structure of beta-fructosidase (invertase) from Thermotoga maritima |
| 关键词 keywords | INVERTASE, GLYCOSYL HYDROLASE FAMILY 32, SUCROSE DEGRADATION, BETA-PROPELLER, 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 | 50.04 Å |
| 回转半径 Rg (电子) rg_electron | 49.67 Å |
| 零角强度 I(0) i0 | 1295870000.00 |
| 分子量 molecular_weight | 300960.0 kDa |
| 排除体积 excluded_volume | 376500 ų |
| 包络体积 envelope_volume | 511380 ų |
| 水化壳体积 shell_volume | 86669 ų |
| 包络直径 envelope_diameter | 171.8 Å |
| 壳层 Rg shell_rg | 52.77 Å |
| 包络 Rg envelope_rg | 48.87 Å |
| 形状 Rg shape_rg | 49.65 Å |
| 总 Rg total_rg | 49.87 Å |
| 总原子数 total_atoms | 21240 |
| 残基数 n_residues | 2592 |
| 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 | 168.4 Å |
| Rg (实空间) rg_real | 50.07 Å |
| Rg 误差 (实空间) rg_real_error | 1.93 Å |
| I(0) (实空间) i0_real | 1.2960e+09 |
| I(0) 误差 (实空间) i0_real_error | 2.6310e+07 |
| Rg (倒空间) rg_reciprocal | 50.00 Å |
| I(0) (倒空间) i0_reciprocal | 1296000000.0000 |
| 解质量估计 total_estimate | 0.8648 |
| 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 | 59.8 Å |
| 偏度 Skewness skewness | 0.362 |
| 峰度 Kurtosis kurtosis | -0.322 |
| 角度范围 angular_range | — – 0.1550 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 73980000.0000 |
| 实空间数据点数 n_real_points | 32 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.738 |
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) 24 domains
SCOP 2.08 (12 domains)
| 结构域编号 domain_id | d1uypa1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.29 — Concanavalin A-like lectins/glucanases |
| 超家族 Superfamily superfamily | b.29.1 — Concanavalin A-like lectins/glucanases |
| 家族 Family family | b.29.1.19 — Glycosyl hydrolases family 32 C-terminal domain |
| 结构域编号 domain_id | d1uypa2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.67 — 5-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.67.2 — Arabinanase/levansucrase/invertase |
| 家族 Family family | b.67.2.3 — Glycosyl hydrolases family 32 N-terminal domain |
| 结构域编号 domain_id | d1uypb1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.29 — Concanavalin A-like lectins/glucanases |
| 超家族 Superfamily superfamily | b.29.1 — Concanavalin A-like lectins/glucanases |
| 家族 Family family | b.29.1.19 — Glycosyl hydrolases family 32 C-terminal domain |
| 结构域编号 domain_id | d1uypb2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.67 — 5-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.67.2 — Arabinanase/levansucrase/invertase |
| 家族 Family family | b.67.2.3 — Glycosyl hydrolases family 32 N-terminal domain |
| 结构域编号 domain_id | d1uypc1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.29 — Concanavalin A-like lectins/glucanases |
| 超家族 Superfamily superfamily | b.29.1 — Concanavalin A-like lectins/glucanases |
| 家族 Family family | b.29.1.19 — Glycosyl hydrolases family 32 C-terminal domain |
| 结构域编号 domain_id | d1uypc2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.67 — 5-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.67.2 — Arabinanase/levansucrase/invertase |
| 家族 Family family | b.67.2.3 — Glycosyl hydrolases family 32 N-terminal domain |
| 结构域编号 domain_id | d1uypd1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.29 — Concanavalin A-like lectins/glucanases |
| 超家族 Superfamily superfamily | b.29.1 — Concanavalin A-like lectins/glucanases |
| 家族 Family family | b.29.1.19 — Glycosyl hydrolases family 32 C-terminal domain |
| 结构域编号 domain_id | d1uypd2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.67 — 5-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.67.2 — Arabinanase/levansucrase/invertase |
| 家族 Family family | b.67.2.3 — Glycosyl hydrolases family 32 N-terminal domain |
| 结构域编号 domain_id | d1uype1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.29 — Concanavalin A-like lectins/glucanases |
| 超家族 Superfamily superfamily | b.29.1 — Concanavalin A-like lectins/glucanases |
| 家族 Family family | b.29.1.19 — Glycosyl hydrolases family 32 C-terminal domain |
| 结构域编号 domain_id | d1uype2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.67 — 5-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.67.2 — Arabinanase/levansucrase/invertase |
| 家族 Family family | b.67.2.3 — Glycosyl hydrolases family 32 N-terminal domain |
| 结构域编号 domain_id | d1uypf1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.29 — Concanavalin A-like lectins/glucanases |
| 超家族 Superfamily superfamily | b.29.1 — Concanavalin A-like lectins/glucanases |
| 家族 Family family | b.29.1.19 — Glycosyl hydrolases family 32 C-terminal domain |
| 结构域编号 domain_id | d1uypf2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.67 — 5-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.67.2 — Arabinanase/levansucrase/invertase |
| 家族 Family family | b.67.2.3 — Glycosyl hydrolases family 32 N-terminal domain |
CATH v4.4 (12 domains)
| 结构域编号 domain_id | 1uypA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 115 — 5 Propeller |
| 拓扑 Topology topology | 10 — Tachylectin-2; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Glycosyl hydrolase domain; family 43 |
| 结构域编号 domain_id | 1uypA02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 560 — Exo-inulinase; domain 1 |
| 结构域编号 domain_id | 1uypB01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 115 — 5 Propeller |
| 拓扑 Topology topology | 10 — Tachylectin-2; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Glycosyl hydrolase domain; family 43 |
| 结构域编号 domain_id | 1uypB02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 560 — Exo-inulinase; domain 1 |
| 结构域编号 domain_id | 1uypC01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 115 — 5 Propeller |
| 拓扑 Topology topology | 10 — Tachylectin-2; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Glycosyl hydrolase domain; family 43 |
| 结构域编号 domain_id | 1uypC02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 560 — Exo-inulinase; domain 1 |
| 结构域编号 domain_id | 1uypD01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 115 — 5 Propeller |
| 拓扑 Topology topology | 10 — Tachylectin-2; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Glycosyl hydrolase domain; family 43 |
| 结构域编号 domain_id | 1uypD02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 560 — Exo-inulinase; domain 1 |
| 结构域编号 domain_id | 1uypE01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 115 — 5 Propeller |
| 拓扑 Topology topology | 10 — Tachylectin-2; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Glycosyl hydrolase domain; family 43 |
| 结构域编号 domain_id | 1uypE02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 560 — Exo-inulinase; domain 1 |
| 结构域编号 domain_id | 1uypF01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 115 — 5 Propeller |
| 拓扑 Topology topology | 10 — Tachylectin-2; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Glycosyl hydrolase domain; family 43 |
| 结构域编号 domain_id | 1uypF02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 560 — Exo-inulinase; domain 1 |