2gtq
Crystal structure of aminopeptidase N from human pathogen Neisseria meningitidis
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 | 2gtq |
| 沉积日期 deposition_date | 2006-04-28 |
| 结构标题 title | Crystal structure of aminopeptidase N from human pathogen Neisseria meningitidis |
| 关键词 keywords | ;alanine aminopeptidase, aminopeptidase N, M1 family peptidases, MCSG, PSI-2, Structural Genomics, Protein Structure Initiative, Midwest Center for Structural Genomics, 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 | 28.87 Å |
| 回转半径 Rg (电子) rg_electron | 28.00 Å |
| 零角强度 I(0) i0 | 170378000.00 |
| 分子量 molecular_weight | 99723.0 kDa |
| 排除体积 excluded_volume | 122780 ų |
| 包络体积 envelope_volume | 148780 ų |
| 水化壳体积 shell_volume | 42722 ų |
| 包络直径 envelope_diameter | 98.8 Å |
| 壳层 Rg shell_rg | 36.64 Å |
| 包络 Rg envelope_rg | 28.12 Å |
| 形状 Rg shape_rg | 28.02 Å |
| 总 Rg total_rg | 28.71 Å |
| 总原子数 total_atoms | 6946 |
| 残基数 n_residues | 846 |
| 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 | 92.3 Å |
| Rg (实空间) rg_real | 28.75 Å |
| Rg 误差 (实空间) rg_real_error | 0.54 Å |
| I(0) (实空间) i0_real | 1.7040e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.5820e+06 |
| Rg (倒空间) rg_reciprocal | 28.80 Å |
| I(0) (倒空间) i0_reciprocal | 170400000.0000 |
| 解质量估计 total_estimate | 0.8882 |
| 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 | 36.9 Å |
| 偏度 Skewness skewness | 0.247 |
| 峰度 Kurtosis kurtosis | -0.289 |
| 角度范围 angular_range | — – 0.2750 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 54840000.0000 |
| 实空间数据点数 n_real_points | 56 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.861; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.964 |
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) 9 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d2gtqa1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.98 — Zn aminopeptidase N-terminal domain |
| 超家族 Superfamily superfamily | b.98.1 — Zn aminopeptidase N-terminal domain |
| 家族 Family family | b.98.1.1 — Zn aminopeptidase N-terminal domain |
| 结构域编号 domain_id | d2gtqa2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.92 — Zincin-like |
| 超家族 Superfamily superfamily | d.92.1 — Metalloproteases ('zincins'), catalytic domain |
| 家族 Family family | d.92.1.13 — Zn aminopeptidase catalytic domain |
| 结构域编号 domain_id | d2gtqa3 |
| 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.1.30 — Zn aminopeptidase insert domain |
| 家族 Family family | b.1.30.1 — Zn aminopeptidase insert domain |
| 结构域编号 domain_id | d2gtqa4 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.118 — alpha-alpha superhelix |
| 超家族 Superfamily superfamily | a.118.1 — ARM repeat |
| 家族 Family family | a.118.1.27 — Aminopeptidase N (APN) C-terminal-like |
CATH v4.4 (5 domains)
| 结构域编号 domain_id | 2gtqA01 |
| 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 | 1730 — tricorn interacting facor f3 domain |
| 结构域编号 domain_id | 2gtqA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 2010 — Zincin-like |
| 同源超家族 H-superfamily homologous superfamily | 30 — |
| 结构域编号 domain_id | 2gtqA03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 390 — Neutral Protease; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Neutral Protease Domain 2 |
| 结构域编号 domain_id | 2gtqA04 |
| 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 | 1840 — Aminopeptidase N, middle-beta domain |
| 结构域编号 domain_id | 2gtqA05 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 25 — Alpha Horseshoe |
| 拓扑 Topology topology | 50 — Zincin-like fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — Peptidase M1, alanyl aminopeptidase, C-terminal domain |