1u8c
A novel adaptation of the integrin PSI domain revealed from its crystal structure
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 | 1u8c |
| 沉积日期 deposition_date | 2004-08-05 |
| 结构标题 title | A novel adaptation of the integrin PSI domain revealed from its crystal structure |
| 关键词 keywords | PSI domain, integrin, vitronectrin receptor, 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 | 40.43 Å |
| 回转半径 Rg (电子) rg_electron | 39.92 Å |
| 零角强度 I(0) i0 | 469860000.00 |
| 分子量 molecular_weight | 173090.0 kDa |
| 排除体积 excluded_volume | 214910 ų |
| 包络体积 envelope_volume | 301490 ų |
| 水化壳体积 shell_volume | 62572 ų |
| 包络直径 envelope_diameter | 139.3 Å |
| 壳层 Rg shell_rg | 46.15 Å |
| 包络 Rg envelope_rg | 39.18 Å |
| 形状 Rg shape_rg | 39.91 Å |
| 总 Rg total_rg | 40.30 Å |
| 总原子数 total_atoms | 12115 |
| 残基数 n_residues | 1526 |
| 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 | 129.2 Å |
| Rg (实空间) rg_real | 40.29 Å |
| Rg 误差 (实空间) rg_real_error | 1.07 Å |
| I(0) (实空间) i0_real | 4.6990e+08 |
| I(0) 误差 (实空间) i0_real_error | 7.7820e+06 |
| Rg (倒空间) rg_reciprocal | 40.43 Å |
| I(0) (倒空间) i0_reciprocal | 469900000.0000 |
| 解质量估计 total_estimate | 0.8985 |
| 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 | 56.3 Å |
| 偏度 Skewness skewness | 0.148 |
| 峰度 Kurtosis kurtosis | -0.491 |
| 角度范围 angular_range | — – 0.1950 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 49280000.0000 |
| 实空间数据点数 n_real_points | 40 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.915; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.935 |
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) 20 domains
SCOP 2.08 (10 domains)
| 结构域编号 domain_id | d1u8ca1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.15 — Integrin domains |
| 家族 Family family | b.1.15.1 — Integrin domains |
| 结构域编号 domain_id | d1u8ca2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.15 — Integrin domains |
| 家族 Family family | b.1.15.1 — Integrin domains |
| 结构域编号 domain_id | d1u8ca3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.15 — Integrin domains |
| 家族 Family family | b.1.15.1 — Integrin domains |
| 结构域编号 domain_id | d1u8ca4 |
| 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.69.8 — Integrin alpha N-terminal domain |
| 家族 Family family | b.69.8.1 — Integrin alpha N-terminal domain |
| 结构域编号 domain_id | d1u8cb1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.15 — Integrin domains |
| 家族 Family family | b.1.15.1 — Integrin domains |
| 结构域编号 domain_id | d1u8cb2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.62 — vWA-like |
| 超家族 Superfamily superfamily | c.62.1 — vWA-like |
| 家族 Family family | c.62.1.1 — Integrin A (or I) domain |
| 结构域编号 domain_id | d1u8cb3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.200 — Integrin beta tail domain |
| 超家族 Superfamily superfamily | d.200.1 — Integrin beta tail domain |
| 家族 Family family | d.200.1.1 — Integrin beta tail domain |
| 结构域编号 domain_id | d1u8cb4 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.3 — Knottins (small inhibitors, toxins, lectins) |
| 超家族 Superfamily superfamily | g.3.11 — EGF/Laminin |
| 家族 Family family | g.3.11.6 — Integrin beta EGF-like domains |
| 结构域编号 domain_id | d1u8cb5 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.3 — Knottins (small inhibitors, toxins, lectins) |
| 超家族 Superfamily superfamily | g.3.11 — EGF/Laminin |
| 家族 Family family | g.3.11.6 — Integrin beta EGF-like domains |
| 结构域编号 domain_id | d1u8cb6 |
| 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 (10 domains)
| 结构域编号 domain_id | 1u8cA01 |
| 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 | 130 — Integrin alpha, N-terminal |
| 结构域编号 domain_id | 1u8cA02 |
| 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 | 1460 — Integrin domains. Chain A, domain 2 |
| 结构域编号 domain_id | 1u8cA03 |
| 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 | 1u8cA04 |
| 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 | 1530 — ntegrin, alpha v. Chain A, domain 4 |
| 结构域编号 domain_id | 1u8cB01 |
| 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 | 1u8cB02 |
| 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 | 1u8cB03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 410 — von Willebrand factor, type A domain |
| 结构域编号 domain_id | 1u8cB04 |
| 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 |
| 结构域编号 domain_id | 1u8cB05 |
| 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 |
| 结构域编号 domain_id | 1u8cB06 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 1240 — Hormone receptor fold |
| 同源超家族 H-superfamily homologous superfamily | 30 — |