1oan
Crystal structure of the dengue 2 virus envelope protein
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 | 1oan |
| 沉积日期 deposition_date | 2003-01-16 |
| 结构标题 title | Crystal structure of the dengue 2 virus envelope protein |
| 关键词 keywords | GLYCOPROTEIN, DENGUE VIRUS, MEMBRANE FUSION, FLAVIVIRUS, FUSION PEPTIDE, LOW-PH CONFORMATIONAL CHANGE; GLYCOPROTEIN |
| 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 | 42.52 Å |
| 回转半径 Rg (电子) rg_electron | 43.53 Å |
| 零角强度 I(0) i0 | 122813000.00 |
| 分子量 molecular_weight | 89392.0 kDa |
| 排除体积 excluded_volume | 111830 ų |
| 包络体积 envelope_volume | 153630 ų |
| 水化壳体积 shell_volume | 33867 ų |
| 包络直径 envelope_diameter | 155.4 Å |
| 壳层 Rg shell_rg | 40.30 Å |
| 包络 Rg envelope_rg | 43.30 Å |
| 形状 Rg shape_rg | 43.53 Å |
| 总 Rg total_rg | 43.36 Å |
| 总原子数 total_atoms | 6251 |
| 残基数 n_residues | 788 |
| 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 | 144.5 Å |
| Rg (实空间) rg_real | 43.20 Å |
| Rg 误差 (实空间) rg_real_error | 1.83 Å |
| I(0) (实空间) i0_real | 1.2280e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.2620e+06 |
| Rg (倒空间) rg_reciprocal | 42.52 Å |
| I(0) (倒空间) i0_reciprocal | 122700000.0000 |
| 解质量估计 total_estimate | 0.7342 |
| 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 | 31.2 Å |
| 偏度 Skewness skewness | 0.620 |
| 峰度 Kurtosis kurtosis | -0.388 |
| 角度范围 angular_range | — – 0.1850 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 7166000.0000 |
| 实空间数据点数 n_real_points | 38 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.618; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.454; Smooth: 0.234 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (5)
6. 折叠分类 (SCOP + CATH) 12 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1oana1 |
| 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.1.18 — E set domains |
| 家族 Family family | b.1.18.4 — Class II viral fusion proteins C-terminal domain |
| 结构域编号 domain_id | d1oana2 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.10 — Viral glycoprotein, central and dimerisation domains |
| 超家族 Superfamily superfamily | f.10.1 — Viral glycoprotein, central and dimerisation domains |
| 家族 Family family | f.10.1.1 — Viral glycoprotein, central and dimerisation domains |
| 结构域编号 domain_id | d1oanb1 |
| 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.1.18 — E set domains |
| 家族 Family family | b.1.18.4 — Class II viral fusion proteins C-terminal domain |
| 结构域编号 domain_id | d1oanb2 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.10 — Viral glycoprotein, central and dimerisation domains |
| 超家族 Superfamily superfamily | f.10.1 — Viral glycoprotein, central and dimerisation domains |
| 家族 Family family | f.10.1.1 — Viral glycoprotein, central and dimerisation domains |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 1oanA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 98 — Tick-borne Encephalitis virus Glycoprotein; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tick-borne Encephalitis virus Glycoprotein, domain 1 |
| 结构域编号 domain_id | 1oanA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 67 — Viral Envelope Glycoprotein; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Viral Envelope Glycoprotein, domain 2 |
| 结构域编号 domain_id | 1oanA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 387 — Viral Envelope Glycoprotein; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Viral Envelope Glycoprotein, domain 3 |
| 结构域编号 domain_id | 1oanA04 |
| 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 | 350 — |
| 结构域编号 domain_id | 1oanB01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 98 — Tick-borne Encephalitis virus Glycoprotein; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Tick-borne Encephalitis virus Glycoprotein, domain 1 |
| 结构域编号 domain_id | 1oanB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 67 — Viral Envelope Glycoprotein; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Viral Envelope Glycoprotein, domain 2 |
| 结构域编号 domain_id | 1oanB03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 387 — Viral Envelope Glycoprotein; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Viral Envelope Glycoprotein, domain 3 |
| 结构域编号 domain_id | 1oanB04 |
| 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 | 350 — |