1olz
The ligand-binding face of the semaphorins revealed by the high resolution crystal structure of SEMA4D
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 | 1olz |
| 沉积日期 deposition_date | 2003-08-19 |
| 结构标题 title | The ligand-binding face of the semaphorins revealed by the high resolution crystal structure of SEMA4D |
| 关键词 keywords | ;DEVELOPMENTAL PROTEIN, CD100, SEMAPHORIN, BETA-PROPELLER, PSI DOMAIN, IG-LIKE DOMAIN, EXTRACELLULAR RECEPTOR, NEUROGENESIS, GLYCOPROTEIN DEVELOPMENTAL PROTEIN, STRUCTURAL PROTEOMICS IN EUROPE, SPINE, STRUCTURAL GENOMICS ;; DEVELOPMENTAL 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 | 37.09 Å |
| 回转半径 Rg (电子) rg_electron | 36.20 Å |
| 零角强度 I(0) i0 | 293138000.00 |
| 分子量 molecular_weight | 139440.0 kDa |
| 排除体积 excluded_volume | 174850 ų |
| 包络体积 envelope_volume | 230060 ų |
| 水化壳体积 shell_volume | 51979 ų |
| 包络直径 envelope_diameter | 115.4 Å |
| 壳层 Rg shell_rg | 43.59 Å |
| 包络 Rg envelope_rg | 35.44 Å |
| 形状 Rg shape_rg | 36.19 Å |
| 总 Rg total_rg | 36.73 Å |
| 总原子数 total_atoms | 9828 |
| 残基数 n_residues | 1244 |
| 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 | 112.2 Å |
| Rg (实空间) rg_real | 36.88 Å |
| Rg 误差 (实空间) rg_real_error | 0.63 Å |
| I(0) (实空间) i0_real | 2.9310e+08 |
| I(0) 误差 (实空间) i0_real_error | 4.1560e+06 |
| Rg (倒空间) rg_reciprocal | 37.02 Å |
| I(0) (倒空间) i0_reciprocal | 293200000.0000 |
| 解质量估计 total_estimate | 0.9099 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 49.6 Å |
| 偏度 Skewness skewness | 0.048 |
| 峰度 Kurtosis kurtosis | -0.680 |
| 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 | 29230000.0000 |
| 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: 0.974; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.907 |
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) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1olza1 |
| 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.1.1 — Immunoglobulin |
| 家族 Family family | b.1.1.4 — I set domains |
| 结构域编号 domain_id | d1olza2 |
| 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 | d1olza3 |
| 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 |
| 结构域编号 domain_id | d1olzb1 |
| 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.1.1 — Immunoglobulin |
| 家族 Family family | b.1.1.4 — I set domains |
| 结构域编号 domain_id | d1olzb2 |
| 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 | d1olzb3 |
| 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 (6 domains)
| 结构域编号 domain_id | 1olzA01 |
| 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 | 1olzA02 |
| 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 | 1olzA03 |
| 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 | 10 — Immunoglobulins |
| 结构域编号 domain_id | 1olzB01 |
| 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 | 1olzB02 |
| 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 | 1olzB03 |
| 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 | 10 — Immunoglobulins |