1vfm
Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase 2/alpha-cyclodextrin 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 | 1vfm |
| 沉积日期 deposition_date | 2004-04-16 |
| 结构标题 title | Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase 2/alpha-cyclodextrin complex |
| 关键词 keywords | amylase, complex, cyclodextrin, 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 | 33.83 Å |
| 回转半径 Rg (电子) rg_electron | 33.00 Å |
| 零角强度 I(0) i0 | 285431000.00 |
| 分子量 molecular_weight | 136940.0 kDa |
| 排除体积 excluded_volume | 171290 ų |
| 包络体积 envelope_volume | 204700 ų |
| 水化壳体积 shell_volume | 50728 ų |
| 包络直径 envelope_diameter | 114.0 Å |
| 壳层 Rg shell_rg | 40.87 Å |
| 包络 Rg envelope_rg | 32.88 Å |
| 形状 Rg shape_rg | 32.97 Å |
| 总 Rg total_rg | 33.65 Å |
| 总原子数 total_atoms | 9686 |
| 残基数 n_residues | 1170 |
| 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 | 107.5 Å |
| Rg (实空间) rg_real | 33.76 Å |
| Rg 误差 (实空间) rg_real_error | 0.75 Å |
| I(0) (实空间) i0_real | 2.8540e+08 |
| I(0) 误差 (实空间) i0_real_error | 4.9870e+06 |
| Rg (倒空间) rg_reciprocal | 33.81 Å |
| I(0) (倒空间) i0_reciprocal | 285400000.0000 |
| 解质量估计 total_estimate | 0.8984 |
| 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 | 38.9 Å |
| 偏度 Skewness skewness | 0.282 |
| 峰度 Kurtosis kurtosis | -0.446 |
| 角度范围 angular_range | — – 0.2350 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 77000000.0000 |
| 实空间数据点数 n_real_points | 48 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.927 |
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) 14 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1vfma1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.18 — E set domains |
| 家族 Family family | b.1.18.0 — automated matches |
| 结构域编号 domain_id | d1vfma2 |
| 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.71.1.0 — automated matches |
| 结构域编号 domain_id | d1vfma3 |
| 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.1.8.1 — Amylase, catalytic domain |
| 结构域编号 domain_id | d1vfmb1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.18 — E set domains |
| 家族 Family family | b.1.18.0 — automated matches |
| 结构域编号 domain_id | d1vfmb2 |
| 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.71.1.0 — automated matches |
| 结构域编号 domain_id | d1vfmb3 |
| 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.1.8.1 — Amylase, catalytic domain |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 1vfmA01 |
| 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 | 10 — Immunoglobulins |
| 结构域编号 domain_id | 1vfmA02 |
| 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 | 1vfmA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 400 — Oligo-1,6-glucosidase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Oligo-1,6-glucosidase; Domain 2 |
| 结构域编号 domain_id | 1vfmA04 |
| 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 | 1vfmB01 |
| 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 | 10 — Immunoglobulins |
| 结构域编号 domain_id | 1vfmB02 |
| 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 | 1vfmB03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 400 — Oligo-1,6-glucosidase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Oligo-1,6-glucosidase; Domain 2 |
| 结构域编号 domain_id | 1vfmB04 |
| 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 |