1qdm
CRYSTAL STRUCTURE OF PROPHYTEPSIN, A ZYMOGEN OF A BARLEY VACUOLAR ASPARTIC PROTEINASE.
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 | 1qdm |
| 沉积日期 deposition_date | 1999-05-19 |
| 结构标题 title | CRYSTAL STRUCTURE OF PROPHYTEPSIN, A ZYMOGEN OF A BARLEY VACUOLAR ASPARTIC PROTEINASE. |
| 关键词 keywords | ASPARTIC PROTEINASES, PHYTEPSIN, SAPOSIN-LIKE DOMAIN, ZYMOGEN STRUCTURE, 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 | 41.25 Å |
| 回转半径 Rg (电子) rg_electron | 40.99 Å |
| 零角强度 I(0) i0 | 254254000.00 |
| 分子量 molecular_weight | 132600.0 kDa |
| 排除体积 excluded_volume | 166670 ų |
| 包络体积 envelope_volume | 222310 ų |
| 水化壳体积 shell_volume | 47378 ų |
| 包络直径 envelope_diameter | 145.9 Å |
| 壳层 Rg shell_rg | 44.19 Å |
| 包络 Rg envelope_rg | 40.34 Å |
| 形状 Rg shape_rg | 40.92 Å |
| 总 Rg total_rg | 41.39 Å |
| 总原子数 total_atoms | 9336 |
| 残基数 n_residues | 1297 |
| 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 | 137.0 Å |
| Rg (实空间) rg_real | 41.42 Å |
| Rg 误差 (实空间) rg_real_error | 1.37 Å |
| I(0) (实空间) i0_real | 2.5430e+08 |
| I(0) 误差 (实空间) i0_real_error | 4.4700e+06 |
| Rg (倒空间) rg_reciprocal | 41.25 Å |
| I(0) (倒空间) i0_reciprocal | 254200000.0000 |
| 解质量估计 total_estimate | 0.6385 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 43.3 Å |
| 偏度 Skewness skewness | 0.396 |
| 峰度 Kurtosis kurtosis | -0.399 |
| 角度范围 angular_range | — – 0.1900 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 17960000.0000 |
| 实空间数据点数 n_real_points | 39 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 0.046; Positv: 1.000; Valcen: 0.953; Smooth: 0.500 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (1)
6. 折叠分类 (SCOP + CATH) 15 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1qdma1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.64 — Saposin-like |
| 超家族 Superfamily superfamily | a.64.1 — Saposin |
| 家族 Family family | a.64.1.2 — Swaposin |
| 结构域编号 domain_id | d1qdma2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.50 — Acid proteases |
| 超家族 Superfamily superfamily | b.50.1 — Acid proteases |
| 家族 Family family | b.50.1.2 — Pepsin-like |
| 结构域编号 domain_id | d1qdmb1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.64 — Saposin-like |
| 超家族 Superfamily superfamily | a.64.1 — Saposin |
| 家族 Family family | a.64.1.2 — Swaposin |
| 结构域编号 domain_id | d1qdmb2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.50 — Acid proteases |
| 超家族 Superfamily superfamily | b.50.1 — Acid proteases |
| 家族 Family family | b.50.1.2 — Pepsin-like |
| 结构域编号 domain_id | d1qdmc1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.64 — Saposin-like |
| 超家族 Superfamily superfamily | a.64.1 — Saposin |
| 家族 Family family | a.64.1.2 — Swaposin |
| 结构域编号 domain_id | d1qdmc2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.50 — Acid proteases |
| 超家族 Superfamily superfamily | b.50.1 — Acid proteases |
| 家族 Family family | b.50.1.2 — Pepsin-like |
CATH v4.4 (9 domains)
| 结构域编号 domain_id | 1qdmA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 70 — Cathepsin D, subunit A; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acid Proteases |
| 结构域编号 domain_id | 1qdmA02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 70 — Cathepsin D, subunit A; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acid Proteases |
| 结构域编号 domain_id | 1qdmA03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 225 — NK-Lysin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Saposin-like |
| 结构域编号 domain_id | 1qdmB01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 70 — Cathepsin D, subunit A; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acid Proteases |
| 结构域编号 domain_id | 1qdmB02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 70 — Cathepsin D, subunit A; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acid Proteases |
| 结构域编号 domain_id | 1qdmB03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 225 — NK-Lysin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Saposin-like |
| 结构域编号 domain_id | 1qdmC01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 70 — Cathepsin D, subunit A; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acid Proteases |
| 结构域编号 domain_id | 1qdmC02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 70 — Cathepsin D, subunit A; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acid Proteases |
| 结构域编号 domain_id | 1qdmC03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 225 — NK-Lysin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Saposin-like |