1yr2
Structural and Mechanistic Analysis of Two Prolyl Endopeptidases: Role of Inter-Domain Dynamics in Catalysis and Specificity
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 | 1yr2 |
| 沉积日期 deposition_date | 2005-02-02 |
| 结构标题 title | Structural and Mechanistic Analysis of Two Prolyl Endopeptidases: Role of Inter-Domain Dynamics in Catalysis and Specificity |
| 关键词 keywords | prolyl endopeptidase, mechanistic study, celiac sprue, 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 | 29.41 Å |
| 回转半径 Rg (电子) rg_electron | 28.47 Å |
| 零角强度 I(0) i0 | 87487800.00 |
| 分子量 molecular_weight | 74227.0 kDa |
| 排除体积 excluded_volume | 93106 ų |
| 包络体积 envelope_volume | 121000 ų |
| 水化壳体积 shell_volume | 35327 ų |
| 包络直径 envelope_diameter | 92.9 Å |
| 壳层 Rg shell_rg | 36.32 Å |
| 包络 Rg envelope_rg | 27.78 Å |
| 形状 Rg shape_rg | 28.46 Å |
| 总 Rg total_rg | 29.28 Å |
| 总原子数 total_atoms | 5263 |
| 残基数 n_residues | 680 |
| 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 | 90.3 Å |
| Rg (实空间) rg_real | 29.31 Å |
| Rg 误差 (实空间) rg_real_error | 0.50 Å |
| I(0) (实空间) i0_real | 8.7490e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.2570e+06 |
| Rg (倒空间) rg_reciprocal | 29.35 Å |
| I(0) (倒空间) i0_reciprocal | 87490000.0000 |
| 解质量估计 total_estimate | 0.9142 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 35.1 Å |
| 偏度 Skewness skewness | 0.161 |
| 峰度 Kurtosis kurtosis | -0.640 |
| 角度范围 angular_range | — – 0.2700 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 10990000.0000 |
| 实空间数据点数 n_real_points | 55 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.972; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.964 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (3)
6. 折叠分类 (SCOP + CATH) 5 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d1yr2a1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.69 — 7-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.69.7 — Peptidase/esterase 'gauge' domain |
| 家族 Family family | b.69.7.0 — automated matches |
| 结构域编号 domain_id | d1yr2a2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.69 — alpha/beta-Hydrolases |
| 超家族 Superfamily superfamily | c.69.1 — alpha/beta-Hydrolases |
| 家族 Family family | c.69.1.0 — automated matches |
| 结构域编号 domain_id | d1yr2a3 |
| 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 (2 domains)
| 结构域编号 domain_id | 1yr2A01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 1820 — Alpha/Beta hydrolase fold, catalytic domain |
| 结构域编号 domain_id | 1yr2A02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 130 — 7 Propeller |
| 拓扑 Topology topology | 10 — Methylamine Dehydrogenase; Chain H |
| 同源超家族 H-superfamily homologous superfamily | 120 — Prolyl oligopeptidase, N-terminal domain |