1nu9
Staphylocoagulase-Prethrombin-2 complex
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 | 1nu9 |
| 沉积日期 deposition_date | 2003-01-31 |
| 结构标题 title | Staphylocoagulase-Prethrombin-2 complex |
| 关键词 keywords | Thrombin non-proteolytic activator, endocarditis, hydrolase-hydrolase inhibitor complex, protein binding; 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 | 45.79 Å |
| 回转半径 Rg (电子) rg_electron | 46.16 Å |
| 零角强度 I(0) i0 | 533385000.00 |
| 分子量 molecular_weight | 125630.0 kDa |
| 排除体积 excluded_volume | 120630 ų |
| 包络体积 envelope_volume | 243560 ų |
| 水化壳体积 shell_volume | 45871 ų |
| 包络直径 envelope_diameter | 152.8 Å |
| 壳层 Rg shell_rg | 48.48 Å |
| 包络 Rg envelope_rg | 44.73 Å |
| 形状 Rg shape_rg | 46.25 Å |
| 总 Rg total_rg | 46.09 Å |
| 总原子数 total_atoms | 9460 |
| 残基数 n_residues | 1052 |
| 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 | 152.1 Å |
| Rg (实空间) rg_real | 46.21 Å |
| Rg 误差 (实空间) rg_real_error | 1.55 Å |
| I(0) (实空间) i0_real | 5.3340e+08 |
| I(0) 误差 (实空间) i0_real_error | 9.4660e+06 |
| Rg (倒空间) rg_reciprocal | 45.80 Å |
| I(0) (倒空间) i0_reciprocal | 533100000.0000 |
| 解质量估计 total_estimate | 0.7728 |
| 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 | 31.3 Å |
| 偏度 Skewness skewness | 0.343 |
| 峰度 Kurtosis kurtosis | -0.942 |
| 角度范围 angular_range | — – 0.1700 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 21510000.0000 |
| 实空间数据点数 n_real_points | 35 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.525; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.671; Smooth: 0.796 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (6)
6. 折叠分类 (SCOP + CATH) 14 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1nu9a_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.47 — Trypsin-like serine proteases |
| 超家族 Superfamily superfamily | b.47.1 — Trypsin-like serine proteases |
| 家族 Family family | b.47.1.2 — Eukaryotic proteases |
| 结构域编号 domain_id | d1nu9c1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.8 — immunoglobulin/albumin-binding domain-like |
| 超家族 Superfamily superfamily | a.8.6 — Staphylocoagulase |
| 家族 Family family | a.8.6.1 — Staphylocoagulase |
| 结构域编号 domain_id | d1nu9c2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.8 — immunoglobulin/albumin-binding domain-like |
| 超家族 Superfamily superfamily | a.8.6 — Staphylocoagulase |
| 家族 Family family | a.8.6.1 — Staphylocoagulase |
| 结构域编号 domain_id | d1nu9d_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.47 — Trypsin-like serine proteases |
| 超家族 Superfamily superfamily | b.47.1 — Trypsin-like serine proteases |
| 家族 Family family | b.47.1.2 — Eukaryotic proteases |
| 结构域编号 domain_id | d1nu9f1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.8 — immunoglobulin/albumin-binding domain-like |
| 超家族 Superfamily superfamily | a.8.6 — Staphylocoagulase |
| 家族 Family family | a.8.6.1 — Staphylocoagulase |
| 结构域编号 domain_id | d1nu9f2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.8 — immunoglobulin/albumin-binding domain-like |
| 超家族 Superfamily superfamily | a.8.6 — Staphylocoagulase |
| 家族 Family family | a.8.6.1 — Staphylocoagulase |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 1nu9A01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 10 — Thrombin, subunit H |
| 同源超家族 H-superfamily homologous superfamily | 10 — Trypsin-like serine proteases |
| 结构域编号 domain_id | 1nu9A02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 10 — Thrombin, subunit H |
| 同源超家族 H-superfamily homologous superfamily | 10 — Trypsin-like serine proteases |
| 结构域编号 domain_id | 1nu9C01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 750 — Staphylcoagulase, helix bundle domain 1 |
| 结构域编号 domain_id | 1nu9C02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 760 — Staphylcoagulase, helix bundle, domain 2 |
| 结构域编号 domain_id | 1nu9D01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 10 — Thrombin, subunit H |
| 同源超家族 H-superfamily homologous superfamily | 10 — Trypsin-like serine proteases |
| 结构域编号 domain_id | 1nu9D02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 10 — Thrombin, subunit H |
| 同源超家族 H-superfamily homologous superfamily | 10 — Trypsin-like serine proteases |
| 结构域编号 domain_id | 1nu9F01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 750 — Staphylcoagulase, helix bundle domain 1 |
| 结构域编号 domain_id | 1nu9F02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 760 — Staphylcoagulase, helix bundle, domain 2 |