2cbi
Structure of the Clostridium perfringens NagJ family 84 glycoside hydrolase, a homologue of human O-GlcNAcase
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 | 2cbi |
| 沉积日期 deposition_date | 2006-01-04 |
| 结构标题 title | Structure of the Clostridium perfringens NagJ family 84 glycoside hydrolase, a homologue of human O-GlcNAcase |
| 关键词 keywords | O-GLCNAC, FAMILY 84 GLYCOSIDE HYDROLASES, GLYCOSIDE HYDROLASE, HYALURONIDASES, CARBOHYDRATES, 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 | 39.63 Å |
| 回转半径 Rg (电子) rg_electron | 39.08 Å |
| 零角强度 I(0) i0 | 275992000.00 |
| 分子量 molecular_weight | 132280.0 kDa |
| 排除体积 excluded_volume | 163740 ų |
| 包络体积 envelope_volume | 213260 ų |
| 水化壳体积 shell_volume | 46076 ų |
| 包络直径 envelope_diameter | 168.2 Å |
| 壳层 Rg shell_rg | 43.71 Å |
| 包络 Rg envelope_rg | 40.24 Å |
| 形状 Rg shape_rg | 38.95 Å |
| 总 Rg total_rg | 39.77 Å |
| 总原子数 total_atoms | 9281 |
| 残基数 n_residues | 1168 |
| 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 | 154.0 Å |
| Rg (实空间) rg_real | 40.01 Å |
| Rg 误差 (实空间) rg_real_error | 2.44 Å |
| I(0) (实空间) i0_real | 2.7600e+08 |
| I(0) 误差 (实空间) i0_real_error | 6.0420e+06 |
| Rg (倒空间) rg_reciprocal | 39.78 Å |
| I(0) (倒空间) i0_reciprocal | 275900000.0000 |
| 解质量估计 total_estimate | 0.7001 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 3 |
| 主峰位置 r_peak_primary | 38.5 Å |
| 偏度 Skewness skewness | 0.514 |
| 峰度 Kurtosis kurtosis | -0.246 |
| 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 | 41610000.0000 |
| 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: 0.515; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.554; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (7)
6. 折叠分类 (SCOP + CATH) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d2cbia1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.246 — Hyaluronidase domain-like |
| 超家族 Superfamily superfamily | a.246.1 — Hyaluronidase post-catalytic domain-like |
| 家族 Family family | a.246.1.1 — Hyaluronidase post-catalytic domain-like |
| 结构域编号 domain_id | d2cbia2 |
| 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.1.8.10 — alpha-D-glucuronidase/Hyaluronidase catalytic domain |
| 结构域编号 domain_id | d2cbia3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.92 — Zincin-like |
| 超家族 Superfamily superfamily | d.92.2 — beta-N-acetylhexosaminidase-like domain |
| 家族 Family family | d.92.2.3 — Hyaluronidase N-terminal domain-like |
| 结构域编号 domain_id | d2cbib1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.246 — Hyaluronidase domain-like |
| 超家族 Superfamily superfamily | a.246.1 — Hyaluronidase post-catalytic domain-like |
| 家族 Family family | a.246.1.1 — Hyaluronidase post-catalytic domain-like |
| 结构域编号 domain_id | d2cbib2 |
| 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.1.8.10 — alpha-D-glucuronidase/Hyaluronidase catalytic domain |
| 结构域编号 domain_id | d2cbib3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.92 — Zincin-like |
| 超家族 Superfamily superfamily | d.92.2 — beta-N-acetylhexosaminidase-like domain |
| 家族 Family family | d.92.2.3 — Hyaluronidase N-terminal domain-like |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 2cbiA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 379 — Chitobiase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Chitobiase/beta-hexosaminidase domain 2-like |
| 结构域编号 domain_id | 2cbiA02 |
| 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 | 2cbiA03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 460 — Hyaluronidase post-catalytic domain-like |
| 结构域编号 domain_id | 2cbiB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 379 — Chitobiase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Chitobiase/beta-hexosaminidase domain 2-like |
| 结构域编号 domain_id | 2cbiB02 |
| 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 | 2cbiB03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 460 — Hyaluronidase post-catalytic domain-like |