1oke
Crystal structure of the dengue 2 virus envelope protein in complex with n-octyl-beta-D-glucoside
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 | 1oke |
| 沉积日期 deposition_date | 2003-07-22 |
| 结构标题 title | Crystal structure of the dengue 2 virus envelope protein in complex with n-octyl-beta-D-glucoside |
| 关键词 keywords | VIRAL PROTEIN, MEMBRANE FUSION, FLAVIVIRUS, FUSION PEPTIDE, LOW-PH CONFORMATIONAL CHANGE, CLASS 2 FUSION PROTEIN; VIRAL 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 | 42.15 Å |
| 回转半径 Rg (电子) rg_electron | 43.06 Å |
| 零角强度 I(0) i0 | 123835000.00 |
| 分子量 molecular_weight | 89954.0 kDa |
| 排除体积 excluded_volume | 112630 ų |
| 包络体积 envelope_volume | 153760 ų |
| 水化壳体积 shell_volume | 34135 ų |
| 包络直径 envelope_diameter | 154.1 Å |
| 壳层 Rg shell_rg | 40.28 Å |
| 包络 Rg envelope_rg | 42.93 Å |
| 形状 Rg shape_rg | 43.06 Å |
| 总 Rg total_rg | 42.88 Å |
| 总原子数 total_atoms | 6290 |
| 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 | 42.81 Å |
| Rg 误差 (实空间) rg_real_error | 1.89 Å |
| I(0) (实空间) i0_real | 1.2380e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.3720e+06 |
| Rg (倒空间) rg_reciprocal | 42.15 Å |
| I(0) (倒空间) i0_reciprocal | 123700000.0000 |
| 解质量估计 total_estimate | 0.7331 |
| 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 | 0.628 |
| 峰度 Kurtosis kurtosis | -0.360 |
| 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 | 7488000.0000 |
| 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: 0.602; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.453; Smooth: 0.267 |
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 | d1okea1 |
| 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 | d1okea2 |
| 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 | d1okeb1 |
| 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 | d1okeb2 |
| 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 | 1okeA01 |
| 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 | 1okeA02 |
| 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 | 1okeA03 |
| 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 | 1okeA04 |
| 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 | 1okeB01 |
| 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 | 1okeB02 |
| 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 | 1okeB03 |
| 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 | 1okeB04 |
| 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 — |