1shy
The Crystal Structure of HGF beta-chain in Complex with the Sema Domain of the Met Receptor.
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 | 1shy |
| 沉积日期 deposition_date | 2004-02-26 |
| 结构标题 title | The Crystal Structure of HGF beta-chain in Complex with the Sema Domain of the Met Receptor. |
| 关键词 keywords | protease, sema domain, PSI domain, receptor ectodomain growth factor, GROWTH FACTOR-GROWTH FACTOR RECEPTOR COMPLEX; GROWTH FACTOR/GROWTH FACTOR RECEPTOR |
| 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 | 29.91 Å |
| 回转半径 Rg (电子) rg_electron | 29.09 Å |
| 零角强度 I(0) i0 | 108204000.00 |
| 分子量 molecular_weight | 81600.0 kDa |
| 排除体积 excluded_volume | 101880 ų |
| 包络体积 envelope_volume | 129900 ų |
| 水化壳体积 shell_volume | 37103 ų |
| 包络直径 envelope_diameter | 114.0 Å |
| 壳层 Rg shell_rg | 36.39 Å |
| 包络 Rg envelope_rg | 29.13 Å |
| 形状 Rg shape_rg | 29.05 Å |
| 总 Rg total_rg | 29.92 Å |
| 总原子数 total_atoms | 5735 |
| 残基数 n_residues | 727 |
| 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 | 104.0 Å |
| Rg (实空间) rg_real | 29.88 Å |
| Rg 误差 (实空间) rg_real_error | 0.79 Å |
| I(0) (实空间) i0_real | 1.0820e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.6340e+06 |
| Rg (倒空间) rg_reciprocal | 29.90 Å |
| I(0) (倒空间) i0_reciprocal | 108200000.0000 |
| 解质量估计 total_estimate | 0.8742 |
| 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 | 35.3 Å |
| 偏度 Skewness skewness | 0.316 |
| 峰度 Kurtosis kurtosis | -0.330 |
| 角度范围 angular_range | — – 0.2650 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 21460000.0000 |
| 实空间数据点数 n_real_points | 54 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.807; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.960 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (2)
6. 折叠分类 (SCOP + CATH) 7 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d1shya_ |
| 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 | d1shyb1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.69 — 7-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.69.12 — Sema domain |
| 家族 Family family | b.69.12.1 — Sema domain |
| 结构域编号 domain_id | d1shyb2 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.16 — Trefoil/Plexin domain-like |
| 超家族 Superfamily superfamily | g.16.2 — Plexin repeat |
| 家族 Family family | g.16.2.1 — Plexin repeat |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 1shyA01 |
| 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 | 1shyA02 |
| 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 | 1shyB01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 130 — 7 Propeller |
| 拓扑 Topology topology | 10 — Methylamine Dehydrogenase; Chain H |
| 同源超家族 H-superfamily homologous superfamily | 10 — YVTN repeat-like/Quinoprotein amine dehydrogenase |
| 结构域编号 domain_id | 1shyB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1680 — ligand-binding face of the semaphorins, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — ligand-binding face of the semaphorins, domain 2 |