1y0y
Crystal structure of tetrahedral aminopeptidase from P. horikoshii in complex with amastatin
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 | 1y0y |
| 沉积日期 deposition_date | 2004-11-16 |
| 结构标题 title | Crystal structure of tetrahedral aminopeptidase from P. horikoshii in complex with amastatin |
| 关键词 keywords | aminopeptidase, PDZ, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR |
| 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 | 21.24 Å |
| 回转半径 Rg (电子) rg_electron | 20.33 Å |
| 零角强度 I(0) i0 | 22593200.00 |
| 分子量 molecular_weight | 37423.0 kDa |
| 排除体积 excluded_volume | 47390 ų |
| 包络体积 envelope_volume | 53747 ų |
| 水化壳体积 shell_volume | 22113 ų |
| 包络直径 envelope_diameter | 77.9 Å |
| 壳层 Rg shell_rg | 27.10 Å |
| 包络 Rg envelope_rg | 20.83 Å |
| 形状 Rg shape_rg | 20.34 Å |
| 总 Rg total_rg | 21.19 Å |
| 总原子数 total_atoms | 2631 |
| 残基数 n_residues | 338 |
| 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 | 75.5 Å |
| Rg (实空间) rg_real | 21.25 Å |
| Rg 误差 (实空间) rg_real_error | 0.56 Å |
| I(0) (实空间) i0_real | 2.2590e+07 |
| I(0) 误差 (实空间) i0_real_error | 2.6680e+05 |
| Rg (倒空间) rg_reciprocal | 21.25 Å |
| I(0) (倒空间) i0_reciprocal | 22590000.0000 |
| 解质量估计 total_estimate | 0.8414 |
| 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 | 74.4 Å |
| 偏度 Skewness skewness | 0.452 |
| 峰度 Kurtosis kurtosis | -0.035 |
| 角度范围 angular_range | — – 0.3750 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 6917000.0000 |
| 实空间数据点数 n_real_points | 69 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.665; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.948; Smooth: 0.992 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (4)
6. 折叠分类 (SCOP + CATH) 4 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d1y0ya1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like |
| 超家族 Superfamily superfamily | b.49.3 — Aminopeptidase/glucanase lid domain |
| 家族 Family family | b.49.3.1 — Aminopeptidase/glucanase lid domain |
| 结构域编号 domain_id | d1y0ya3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.56 — Phosphorylase/hydrolase-like |
| 超家族 Superfamily superfamily | c.56.5 — Zn-dependent exopeptidases |
| 家族 Family family | c.56.5.4 — Bacterial dinuclear zinc exopeptidases |
CATH v4.4 (2 domains)
| 结构域编号 domain_id | 1y0yA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 630 — Aminopeptidase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Zn peptidases |
| 结构域编号 domain_id | 1y0yA02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 30 — Elongation Factor Tu (Ef-tu); domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 40 — Peptidase M42, domain 2 |