1gyk
Serum Amyloid P Component co-crystallised with MOBDG at neutral pH
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 | 1gyk |
| 沉积日期 deposition_date | 2002-04-25 |
| 结构标题 title | Serum Amyloid P Component co-crystallised with MOBDG at neutral pH |
| 关键词 keywords | PENTRAXIN, AMYLOID LECTIN, GLYCOPROTEIN, PLASMA, POLYMORPHISM; GLYCOPROTEIN |
| 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 | 36.49 Å |
| 回转半径 Rg (电子) rg_electron | 35.30 Å |
| 零角强度 I(0) i0 | 192314000.00 |
| 分子量 molecular_weight | 117700.0 kDa |
| 排除体积 excluded_volume | 149290 ų |
| 包络体积 envelope_volume | 189050 ų |
| 水化壳体积 shell_volume | 42648 ų |
| 包络直径 envelope_diameter | 106.3 Å |
| 壳层 Rg shell_rg | 44.21 Å |
| 包络 Rg envelope_rg | 34.34 Å |
| 形状 Rg shape_rg | 35.30 Å |
| 总 Rg total_rg | 35.94 Å |
| 总原子数 total_atoms | 8326 |
| 残基数 n_residues | 1020 |
| 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 | 102.3 Å |
| Rg (实空间) rg_real | 36.30 Å |
| Rg 误差 (实空间) rg_real_error | 0.68 Å |
| I(0) (实空间) i0_real | 1.9230e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.0170e+06 |
| Rg (倒空间) rg_reciprocal | 36.42 Å |
| I(0) (倒空间) i0_reciprocal | 192300000.0000 |
| 解质量估计 total_estimate | 0.6336 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 3 |
| 主峰位置 r_peak_primary | 54.7 Å |
| 偏度 Skewness skewness | -0.012 |
| 峰度 Kurtosis kurtosis | -0.843 |
| 角度范围 angular_range | — – 0.2150 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 152200000.0000 |
| 实空间数据点数 n_real_points | 44 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.980; Stabil: 1.000; Sysdev: 0.048; Positv: 1.000; Valcen: 0.998; Smooth: 0.152 |
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) 10 domains
SCOP 2.08 (5 domains)
| 结构域编号 domain_id | d1gyka_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.29 — Concanavalin A-like lectins/glucanases |
| 超家族 Superfamily superfamily | b.29.1 — Concanavalin A-like lectins/glucanases |
| 家族 Family family | b.29.1.5 — Pentraxin (pentaxin) |
| 结构域编号 domain_id | d1gykb_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.29 — Concanavalin A-like lectins/glucanases |
| 超家族 Superfamily superfamily | b.29.1 — Concanavalin A-like lectins/glucanases |
| 家族 Family family | b.29.1.5 — Pentraxin (pentaxin) |
| 结构域编号 domain_id | d1gykc_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.29 — Concanavalin A-like lectins/glucanases |
| 超家族 Superfamily superfamily | b.29.1 — Concanavalin A-like lectins/glucanases |
| 家族 Family family | b.29.1.5 — Pentraxin (pentaxin) |
| 结构域编号 domain_id | d1gykd_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.29 — Concanavalin A-like lectins/glucanases |
| 超家族 Superfamily superfamily | b.29.1 — Concanavalin A-like lectins/glucanases |
| 家族 Family family | b.29.1.5 — Pentraxin (pentaxin) |
| 结构域编号 domain_id | d1gyke_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.29 — Concanavalin A-like lectins/glucanases |
| 超家族 Superfamily superfamily | b.29.1 — Concanavalin A-like lectins/glucanases |
| 家族 Family family | b.29.1.5 — Pentraxin (pentaxin) |
CATH v4.4 (5 domains)
| 结构域编号 domain_id | 1gykA00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 200 — |
| 结构域编号 domain_id | 1gykB00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 200 — |
| 结构域编号 domain_id | 1gykC00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 200 — |
| 结构域编号 domain_id | 1gykD00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 200 — |
| 结构域编号 domain_id | 1gykE00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 200 — |