2i26
Crystal structure analysis of the nurse shark new antigen receptor ancestral variable domain in complex with lysozyme
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 | 2i26 |
| 沉积日期 deposition_date | 2006-08-15 |
| 结构标题 title | Crystal structure analysis of the nurse shark new antigen receptor ancestral variable domain in complex with lysozyme |
| 关键词 keywords | immunoglobulin fold, protein-protein complex, immune system; IMMUNE SYSTEM |
| 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 | 32.65 Å |
| 回转半径 Rg (电子) rg_electron | 32.18 Å |
| 零角强度 I(0) i0 | 125923000.00 |
| 分子量 molecular_weight | 81540.0 kDa |
| 排除体积 excluded_volume | 98832 ų |
| 包络体积 envelope_volume | 131880 ų |
| 水化壳体积 shell_volume | 36053 ų |
| 包络直径 envelope_diameter | 111.3 Å |
| 壳层 Rg shell_rg | 37.33 Å |
| 包络 Rg envelope_rg | 31.50 Å |
| 形状 Rg shape_rg | 32.11 Å |
| 总 Rg total_rg | 32.76 Å |
| 总原子数 total_atoms | 5698 |
| 残基数 n_residues | 736 |
| 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 | 108.5 Å |
| Rg (实空间) rg_real | 32.70 Å |
| Rg 误差 (实空间) rg_real_error | 1.14 Å |
| I(0) (实空间) i0_real | 1.2590e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.1210e+06 |
| Rg (倒空间) rg_reciprocal | 32.68 Å |
| I(0) (倒空间) i0_reciprocal | 125900000.0000 |
| 解质量估计 total_estimate | 0.8881 |
| 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 | 39.8 Å |
| 偏度 Skewness skewness | 0.345 |
| 峰度 Kurtosis kurtosis | -0.402 |
| 角度范围 angular_range | — – 0.2450 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 10990000.0000 |
| 实空间数据点数 n_real_points | 50 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.882; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.929 |
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) 15 domains
SCOP 2.08 (9 domains)
| 结构域编号 domain_id | d2i26l_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.2 — Lysozyme-like |
| 超家族 Superfamily superfamily | d.2.1 — Lysozyme-like |
| 家族 Family family | d.2.1.2 — C-type lysozyme |
| 结构域编号 domain_id | d2i26m_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.2 — Lysozyme-like |
| 超家族 Superfamily superfamily | d.2.1 — Lysozyme-like |
| 家族 Family family | d.2.1.2 — C-type lysozyme |
| 结构域编号 domain_id | d2i26n1 |
| 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.1.1.1 — V set domains (antibody variable domain-like) |
| 结构域编号 domain_id | d2i26n2 |
| 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 | d2i26o2 |
| 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.1.1.1 — V set domains (antibody variable domain-like) |
| 结构域编号 domain_id | d2i26o3 |
| 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 | d2i26p2 |
| 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.1.1.1 — V set domains (antibody variable domain-like) |
| 结构域编号 domain_id | d2i26p3 |
| 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 | d2i26q_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.2 — Lysozyme-like |
| 超家族 Superfamily superfamily | d.2.1 — Lysozyme-like |
| 家族 Family family | d.2.1.2 — C-type lysozyme |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 2i26L00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 530 — Lysozyme |
| 同源超家族 H-superfamily homologous superfamily | 10 — |
| 结构域编号 domain_id | 2i26M00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 530 — Lysozyme |
| 同源超家族 H-superfamily homologous superfamily | 10 — |
| 结构域编号 domain_id | 2i26N00 |
| 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 | 2i26O00 |
| 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 | 2i26P00 |
| 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 | 2i26Q00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 530 — Lysozyme |
| 同源超家族 H-superfamily homologous superfamily | 10 — |