2d39
Trivalent Recognition Unit of Innate Immunity System; Crystal Structure of human M-ficolin Fibrinogen-like Domain
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 | 2d39 |
| 沉积日期 deposition_date | 2005-09-26 |
| 结构标题 title | Trivalent Recognition Unit of Innate Immunity System; Crystal Structure of human M-ficolin Fibrinogen-like Domain |
| 关键词 keywords | Innate immunity system, ficolin, M-ficolin, lectin pathway, 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 | 26.23 Å |
| 回转半径 Rg (电子) rg_electron | 25.08 Å |
| 零角强度 I(0) i0 | 84240100.00 |
| 分子量 molecular_weight | 69804.0 kDa |
| 排除体积 excluded_volume | 86165 ų |
| 包络体积 envelope_volume | 100730 ų |
| 水化壳体积 shell_volume | 32745 ų |
| 包络直径 envelope_diameter | 80.5 Å |
| 壳层 Rg shell_rg | 33.00 Å |
| 包络 Rg envelope_rg | 25.01 Å |
| 形状 Rg shape_rg | 25.07 Å |
| 总 Rg total_rg | 25.92 Å |
| 总原子数 total_atoms | 4929 |
| 残基数 n_residues | 621 |
| 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 | 77.3 Å |
| Rg (实空间) rg_real | 26.07 Å |
| Rg 误差 (实空间) rg_real_error | 0.29 Å |
| I(0) (实空间) i0_real | 8.4240e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.0190e+06 |
| Rg (倒空间) rg_reciprocal | 26.12 Å |
| I(0) (倒空间) i0_reciprocal | 84240000.0000 |
| 解质量估计 total_estimate | 0.9146 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 30.9 Å |
| 偏度 Skewness skewness | 0.108 |
| 峰度 Kurtosis kurtosis | -0.616 |
| 角度范围 angular_range | — – 0.3000 Å−1 |
| 当前正则化参数 α current_alpha | 0.0001 |
| 最高正则化参数 α highest_alpha | 13730000.0000 |
| 实空间数据点数 n_real_points | 61 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.977; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.965 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (3)
6. 折叠分类 (SCOP + CATH) 11 domains
SCOP 2.08 (5 domains)
| 结构域编号 domain_id | d2d39a1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.171 — Fibrinogen C-terminal domain-like |
| 超家族 Superfamily superfamily | d.171.1 — Fibrinogen C-terminal domain-like |
| 家族 Family family | d.171.1.0 — automated matches |
| 结构域编号 domain_id | d2d39a2 |
| 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 | d2d39b1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.171 — Fibrinogen C-terminal domain-like |
| 超家族 Superfamily superfamily | d.171.1 — Fibrinogen C-terminal domain-like |
| 家族 Family family | d.171.1.0 — automated matches |
| 结构域编号 domain_id | d2d39b2 |
| 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 | d2d39c_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.171 — Fibrinogen C-terminal domain-like |
| 超家族 Superfamily superfamily | d.171.1 — Fibrinogen C-terminal domain-like |
| 家族 Family family | d.171.1.0 — automated matches |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 2d39A01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 215 — Gamma Fibrinogen; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Gamma Fibrinogen, chain A, domain 1 |
| 结构域编号 domain_id | 2d39A02 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 |
| 结构域编号 domain_id | 2d39B01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 215 — Gamma Fibrinogen; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Gamma Fibrinogen, chain A, domain 1 |
| 结构域编号 domain_id | 2d39B02 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 |
| 结构域编号 domain_id | 2d39C01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 215 — Gamma Fibrinogen; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Gamma Fibrinogen, chain A, domain 1 |
| 结构域编号 domain_id | 2d39C02 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 |