1yi7
Beta-d-xylosidase (selenomethionine) XYND from Clostridium Acetobutylicum
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 | 1yi7 |
| 沉积日期 deposition_date | 2005-01-11 |
| 结构标题 title | Beta-d-xylosidase (selenomethionine) XYND from Clostridium Acetobutylicum |
| 关键词 keywords | ;Beta-propeller, beta-sandwich, Structural Genomics, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, 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 | 39.12 Å |
| 回转半径 Rg (电子) rg_electron | 38.41 Å |
| 零角强度 I(0) i0 | 924781000.00 |
| 分子量 molecular_weight | 249590.0 kDa |
| 排除体积 excluded_volume | 310910 ų |
| 包络体积 envelope_volume | 378140 ų |
| 水化壳体积 shell_volume | 77331 ų |
| 包络直径 envelope_diameter | 118.6 Å |
| 壳层 Rg shell_rg | 47.89 Å |
| 包络 Rg envelope_rg | 37.85 Å |
| 形状 Rg shape_rg | 38.42 Å |
| 总 Rg total_rg | 38.83 Å |
| 总原子数 total_atoms | 17583 |
| 残基数 n_residues | 2120 |
| 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 | 117.4 Å |
| Rg (实空间) rg_real | 38.78 Å |
| Rg 误差 (实空间) rg_real_error | 0.52 Å |
| I(0) (实空间) i0_real | 9.2480e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.3460e+07 |
| Rg (倒空间) rg_reciprocal | 38.99 Å |
| I(0) (倒空间) i0_reciprocal | 925000000.0000 |
| 解质量估计 total_estimate | 0.6718 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 52.8 Å |
| 偏度 Skewness skewness | 0.046 |
| 峰度 Kurtosis kurtosis | -0.526 |
| 角度范围 angular_range | — – 0.2000 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 973900000.0000 |
| 实空间数据点数 n_real_points | 41 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.966; Smooth: 0.793 |
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 (16 domains)
| 结构域编号 domain_id | d1yi7a1 |
| 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.29.1.23 — Beta-D-xylosidase C-terminal domain-like |
| 结构域编号 domain_id | d1yi7a2 |
| 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.67.2.1 — alpha-L-arabinanase-like |
| 结构域编号 domain_id | d1yi7a3 |
| 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 | d1yi7a4 |
| 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 | d1yi7b1 |
| 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.29.1.23 — Beta-D-xylosidase C-terminal domain-like |
| 结构域编号 domain_id | d1yi7b2 |
| 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.67.2.1 — alpha-L-arabinanase-like |
| 结构域编号 domain_id | d1yi7b3 |
| 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 | d1yi7b4 |
| 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 | d1yi7c1 |
| 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.29.1.23 — Beta-D-xylosidase C-terminal domain-like |
| 结构域编号 domain_id | d1yi7c2 |
| 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.67.2.1 — alpha-L-arabinanase-like |
| 结构域编号 domain_id | d1yi7c3 |
| 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 | d1yi7c4 |
| 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 | d1yi7d1 |
| 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.29.1.23 — Beta-D-xylosidase C-terminal domain-like |
| 结构域编号 domain_id | d1yi7d2 |
| 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.67.2.1 — alpha-L-arabinanase-like |
| 结构域编号 domain_id | d1yi7d3 |
| 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 | d1yi7d4 |
| 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 (8 domains)
| 结构域编号 domain_id | 1yi7A01 |
| 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 | 1yi7A02 |
| 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 | 200 — |
| 结构域编号 domain_id | 1yi7B01 |
| 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 | 1yi7B02 |
| 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 | 200 — |
| 结构域编号 domain_id | 1yi7C01 |
| 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 | 1yi7C02 |
| 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 | 200 — |
| 结构域编号 domain_id | 1yi7D01 |
| 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 | 1yi7D02 |
| 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 | 200 — |