1gyt
E. coli Aminopeptidase A (PepA)
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 | 1gyt |
| 沉积日期 deposition_date | 2002-04-29 |
| 结构标题 title | E. coli Aminopeptidase A (PepA) |
| 关键词 keywords | HYDROLASE, PEPTIDASE, DNA RECOMBINATION, AMINOPEPTIDASE; 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 | 74.36 Å |
| 回转半径 Rg (电子) rg_electron | 74.80 Å |
| 零角强度 I(0) i0 | 6382460000.00 |
| 分子量 molecular_weight | 660980.0 kDa |
| 排除体积 excluded_volume | 821030 ų |
| 包络体积 envelope_volume | 1199400 ų |
| 水化壳体积 shell_volume | 132280 ų |
| 包络直径 envelope_diameter | 248.9 Å |
| 壳层 Rg shell_rg | 74.76 Å |
| 包络 Rg envelope_rg | 72.75 Å |
| 形状 Rg shape_rg | 74.82 Å |
| 总 Rg total_rg | 74.72 Å |
| 总原子数 total_atoms | 46228 |
| 残基数 n_residues | 6036 |
| 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 | 215.6 Å |
| Rg (实空间) rg_real | 74.53 Å |
| Rg 误差 (实空间) rg_real_error | 1.16 Å |
| I(0) (实空间) i0_real | 6.3770e+09 |
| I(0) 误差 (实空间) i0_real_error | 1.1650e+08 |
| Rg (倒空间) rg_reciprocal | 72.99 Å |
| I(0) (倒空间) i0_reciprocal | 6360000000.0000 |
| 解质量估计 total_estimate | 0.8086 |
| 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 | 61.6 Å |
| 偏度 Skewness skewness | 0.343 |
| 峰度 Kurtosis kurtosis | -0.853 |
| 角度范围 angular_range | — – 0.1050 Å−1 |
| 当前正则化参数 α current_alpha | 0.0056 |
| 最高正则化参数 α highest_alpha | 1689000000.0000 |
| 实空间数据点数 n_real_points | 22 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.849; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.000 |
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) 48 domains
SCOP 2.08 (24 domains)
| 结构域编号 domain_id | d1gyta1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.50 — Macro domain-like |
| 超家族 Superfamily superfamily | c.50.1 — Macro domain-like |
| 家族 Family family | c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain |
| 结构域编号 domain_id | d1gyta2 |
| 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.56.5.3 — Leucine aminopeptidase, C-terminal domain |
| 结构域编号 domain_id | d1gytb1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.50 — Macro domain-like |
| 超家族 Superfamily superfamily | c.50.1 — Macro domain-like |
| 家族 Family family | c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain |
| 结构域编号 domain_id | d1gytb2 |
| 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.56.5.3 — Leucine aminopeptidase, C-terminal domain |
| 结构域编号 domain_id | d1gytc1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.50 — Macro domain-like |
| 超家族 Superfamily superfamily | c.50.1 — Macro domain-like |
| 家族 Family family | c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain |
| 结构域编号 domain_id | d1gytc2 |
| 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.56.5.3 — Leucine aminopeptidase, C-terminal domain |
| 结构域编号 domain_id | d1gytd1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.50 — Macro domain-like |
| 超家族 Superfamily superfamily | c.50.1 — Macro domain-like |
| 家族 Family family | c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain |
| 结构域编号 domain_id | d1gytd2 |
| 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.56.5.3 — Leucine aminopeptidase, C-terminal domain |
| 结构域编号 domain_id | d1gyte1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.50 — Macro domain-like |
| 超家族 Superfamily superfamily | c.50.1 — Macro domain-like |
| 家族 Family family | c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain |
| 结构域编号 domain_id | d1gyte2 |
| 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.56.5.3 — Leucine aminopeptidase, C-terminal domain |
| 结构域编号 domain_id | d1gytf1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.50 — Macro domain-like |
| 超家族 Superfamily superfamily | c.50.1 — Macro domain-like |
| 家族 Family family | c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain |
| 结构域编号 domain_id | d1gytf2 |
| 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.56.5.3 — Leucine aminopeptidase, C-terminal domain |
| 结构域编号 domain_id | d1gytg1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.50 — Macro domain-like |
| 超家族 Superfamily superfamily | c.50.1 — Macro domain-like |
| 家族 Family family | c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain |
| 结构域编号 domain_id | d1gytg2 |
| 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.56.5.3 — Leucine aminopeptidase, C-terminal domain |
| 结构域编号 domain_id | d1gyth1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.50 — Macro domain-like |
| 超家族 Superfamily superfamily | c.50.1 — Macro domain-like |
| 家族 Family family | c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain |
| 结构域编号 domain_id | d1gyth2 |
| 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.56.5.3 — Leucine aminopeptidase, C-terminal domain |
| 结构域编号 domain_id | d1gyti1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.50 — Macro domain-like |
| 超家族 Superfamily superfamily | c.50.1 — Macro domain-like |
| 家族 Family family | c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain |
| 结构域编号 domain_id | d1gyti2 |
| 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.56.5.3 — Leucine aminopeptidase, C-terminal domain |
| 结构域编号 domain_id | d1gytj1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.50 — Macro domain-like |
| 超家族 Superfamily superfamily | c.50.1 — Macro domain-like |
| 家族 Family family | c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain |
| 结构域编号 domain_id | d1gytj2 |
| 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.56.5.3 — Leucine aminopeptidase, C-terminal domain |
| 结构域编号 domain_id | d1gytk1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.50 — Macro domain-like |
| 超家族 Superfamily superfamily | c.50.1 — Macro domain-like |
| 家族 Family family | c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain |
| 结构域编号 domain_id | d1gytk2 |
| 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.56.5.3 — Leucine aminopeptidase, C-terminal domain |
| 结构域编号 domain_id | d1gytl1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.50 — Macro domain-like |
| 超家族 Superfamily superfamily | c.50.1 — Macro domain-like |
| 家族 Family family | c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain |
| 结构域编号 domain_id | d1gytl2 |
| 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.56.5.3 — Leucine aminopeptidase, C-terminal domain |
CATH v4.4 (24 domains)
| 结构域编号 domain_id | 1gytA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 220 — Leucine Aminopeptidase, subunit E; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Leucine Aminopeptidase, subunit E, domain 1 |
| 结构域编号 domain_id | 1gytA02 |
| 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 | 1gytB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 220 — Leucine Aminopeptidase, subunit E; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Leucine Aminopeptidase, subunit E, domain 1 |
| 结构域编号 domain_id | 1gytB02 |
| 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 | 1gytC01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 220 — Leucine Aminopeptidase, subunit E; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Leucine Aminopeptidase, subunit E, domain 1 |
| 结构域编号 domain_id | 1gytC02 |
| 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 | 1gytD01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 220 — Leucine Aminopeptidase, subunit E; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Leucine Aminopeptidase, subunit E, domain 1 |
| 结构域编号 domain_id | 1gytD02 |
| 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 | 1gytE01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 220 — Leucine Aminopeptidase, subunit E; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Leucine Aminopeptidase, subunit E, domain 1 |
| 结构域编号 domain_id | 1gytE02 |
| 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 | 1gytF01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 220 — Leucine Aminopeptidase, subunit E; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Leucine Aminopeptidase, subunit E, domain 1 |
| 结构域编号 domain_id | 1gytF02 |
| 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 | 1gytG01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 220 — Leucine Aminopeptidase, subunit E; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Leucine Aminopeptidase, subunit E, domain 1 |
| 结构域编号 domain_id | 1gytG02 |
| 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 | 1gytH01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 220 — Leucine Aminopeptidase, subunit E; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Leucine Aminopeptidase, subunit E, domain 1 |
| 结构域编号 domain_id | 1gytH02 |
| 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 | 1gytI01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 220 — Leucine Aminopeptidase, subunit E; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Leucine Aminopeptidase, subunit E, domain 1 |
| 结构域编号 domain_id | 1gytI02 |
| 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 | 1gytJ01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 220 — Leucine Aminopeptidase, subunit E; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Leucine Aminopeptidase, subunit E, domain 1 |
| 结构域编号 domain_id | 1gytJ02 |
| 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 | 1gytK01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 220 — Leucine Aminopeptidase, subunit E; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Leucine Aminopeptidase, subunit E, domain 1 |
| 结构域编号 domain_id | 1gytK02 |
| 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 | 1gytL01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 220 — Leucine Aminopeptidase, subunit E; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Leucine Aminopeptidase, subunit E, domain 1 |
| 结构域编号 domain_id | 1gytL02 |
| 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 |