1ybo
Crystal structure of the PDZ tandem of human syntenin with syndecan peptide
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 | 1ybo |
| 沉积日期 deposition_date | 2004-12-21 |
| 结构标题 title | Crystal structure of the PDZ tandem of human syntenin with syndecan peptide |
| 关键词 keywords | PDZ domain, scaffolding protein, adhesion complex, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN |
| 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 | 23.05 Å |
| 回转半径 Rg (电子) rg_electron | 22.12 Å |
| 零角强度 I(0) i0 | 23749600.00 |
| 分子量 molecular_weight | 36785.0 kDa |
| 排除体积 excluded_volume | 46034 ų |
| 包络体积 envelope_volume | 56885 ų |
| 水化壳体积 shell_volume | 21706 ų |
| 包络直径 envelope_diameter | 84.5 Å |
| 壳层 Rg shell_rg | 28.53 Å |
| 包络 Rg envelope_rg | 22.44 Å |
| 形状 Rg shape_rg | 22.12 Å |
| 总 Rg total_rg | 22.98 Å |
| 总原子数 total_atoms | 2580 |
| 残基数 n_residues | 337 |
| 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 | 79.0 Å |
| Rg (实空间) rg_real | 23.02 Å |
| Rg 误差 (实空间) rg_real_error | 0.64 Å |
| I(0) (实空间) i0_real | 2.3750e+07 |
| I(0) 误差 (实空间) i0_real_error | 3.4930e+05 |
| Rg (倒空间) rg_reciprocal | 23.03 Å |
| I(0) (倒空间) i0_reciprocal | 23750000.0000 |
| 解质量估计 total_estimate | 0.7936 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 3 |
| 主峰位置 r_peak_primary | 23.1 Å |
| 偏度 Skewness skewness | 0.287 |
| 峰度 Kurtosis kurtosis | -0.363 |
| 角度范围 angular_range | — – 0.3450 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 19400000.0000 |
| 实空间数据点数 n_real_points | 66 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.785; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.000 |
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 (6 domains)
| 结构域编号 domain_id | d1yboa1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.36 — PDZ domain-like |
| 超家族 Superfamily superfamily | b.36.1 — PDZ domain-like |
| 家族 Family family | b.36.1.1 — PDZ domain |
| 结构域编号 domain_id | d1yboa2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.36 — PDZ domain-like |
| 超家族 Superfamily superfamily | b.36.1 — PDZ domain-like |
| 家族 Family family | b.36.1.1 — PDZ domain |
| 结构域编号 domain_id | d1yboa3 |
| 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 |
| 结构域编号 domain_id | d1ybob1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.36 — PDZ domain-like |
| 超家族 Superfamily superfamily | b.36.1 — PDZ domain-like |
| 家族 Family family | b.36.1.1 — PDZ domain |
| 结构域编号 domain_id | d1ybob2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.36 — PDZ domain-like |
| 超家族 Superfamily superfamily | b.36.1 — PDZ domain-like |
| 家族 Family family | b.36.1.1 — PDZ domain |
| 结构域编号 domain_id | d1ybob3 |
| 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 (4 domains)
| 结构域编号 domain_id | 1yboA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 42 — Pdz3 Domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — PDZ domain |
| 结构域编号 domain_id | 1yboA02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 42 — Pdz3 Domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — PDZ domain |
| 结构域编号 domain_id | 1yboB01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 42 — Pdz3 Domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — PDZ domain |
| 结构域编号 domain_id | 1yboB02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 42 — Pdz3 Domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — PDZ domain |