1yuk
The crystal structure of the PSI/Hybrid domain/ I-EGF1 segment from the human integrin beta2 at 1.8 resolution
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 | 1yuk |
| 沉积日期 deposition_date | 2005-02-14 |
| 结构标题 title | The crystal structure of the PSI/Hybrid domain/ I-EGF1 segment from the human integrin beta2 at 1.8 resolution |
| 关键词 keywords | Integrin beta2, hybrid domain, PSI domain, I-EGF domain, crystal structure of PSI/HYBRID/I-EGF1, CELL ADHESION; CELL ADHESION |
| 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 | 23.44 Å |
| 回转半径 Rg (电子) rg_electron | 23.08 Å |
| 零角强度 I(0) i0 | 12053800.00 |
| 分子量 molecular_weight | 24246.0 kDa |
| 排除体积 excluded_volume | 29593 ų |
| 包络体积 envelope_volume | 38082 ų |
| 水化壳体积 shell_volume | 15325 ų |
| 包络直径 envelope_diameter | 84.8 Å |
| 壳层 Rg shell_rg | 27.76 Å |
| 包络 Rg envelope_rg | 23.43 Å |
| 形状 Rg shape_rg | 23.12 Å |
| 总 Rg total_rg | 23.59 Å |
| 总原子数 total_atoms | 1687 |
| 残基数 n_residues | 214 |
| 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 | 87.7 Å |
| Rg (实空间) rg_real | 23.77 Å |
| Rg 误差 (实空间) rg_real_error | 1.14 Å |
| I(0) (实空间) i0_real | 1.2050e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.9530e+05 |
| Rg (倒空间) rg_reciprocal | 23.69 Å |
| I(0) (倒空间) i0_reciprocal | 12050000.0000 |
| 解质量估计 total_estimate | 0.7449 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 18.9 Å |
| 偏度 Skewness skewness | 0.572 |
| 峰度 Kurtosis kurtosis | -0.349 |
| 角度范围 angular_range | — – 0.3400 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 2891000.0000 |
| 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: 0.477; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.250; Smooth: 1.000 |
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) 4 domains
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 1yukA01 |
| 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 |
| 结构域编号 domain_id | 1yukA02 |
| 类 Class class | 6 — Special |
| 架构 Architecture architecture | 20 — Other non-globular |
| 拓扑 Topology topology | 50 — N-terminal domain of TfIIb |
| 同源超家族 H-superfamily homologous superfamily | 10 — |
| 结构域编号 domain_id | 1yukB01 |
| 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 | 1510 — ntegrin, alpha v. Chain A, domain 3 |
| 结构域编号 domain_id | 1yukB02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 10 — Ribbon |
| 拓扑 Topology topology | 25 — Laminin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Laminin |