2df7
Crystal structure of infectious bursal disease virus VP2 subviral particle
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 | 2df7 |
| 沉积日期 deposition_date | 2006-02-27 |
| 结构标题 title | Crystal structure of infectious bursal disease virus VP2 subviral particle |
| 关键词 keywords | icosahedral capsid, immunogen, epitope, surface loop, VIRUS LIKE PARTICLE; VIRUS LIKE PARTICLE |
| 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 | 71.95 Å |
| 回转半径 Rg (电子) rg_electron | 71.35 Å |
| 零角强度 I(0) i0 | 10583600000.00 |
| 分子量 molecular_weight | 887780.0 kDa |
| 排除体积 excluded_volume | 1115700 ų |
| 包络体积 envelope_volume | 1557400 ų |
| 水化壳体积 shell_volume | 173590 ų |
| 包络直径 envelope_diameter | 263.7 Å |
| 壳层 Rg shell_rg | 76.99 Å |
| 包络 Rg envelope_rg | 71.17 Å |
| 形状 Rg shape_rg | 71.35 Å |
| 总 Rg total_rg | 71.42 Å |
| 总原子数 total_atoms | 62511 |
| 残基数 n_residues | 8290 |
| 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 | 269.2 Å |
| Rg (实空间) rg_real | 74.88 Å |
| Rg 误差 (实空间) rg_real_error | 2.22 Å |
| I(0) (实空间) i0_real | 1.0650e+10 |
| I(0) 误差 (实空间) i0_real_error | 2.4660e+08 |
| Rg (倒空间) rg_reciprocal | 72.00 Å |
| I(0) (倒空间) i0_reciprocal | 10580000000.0000 |
| 解质量估计 total_estimate | 0.8615 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 85.6 Å |
| 偏度 Skewness skewness | 0.521 |
| 峰度 Kurtosis kurtosis | 0.179 |
| 角度范围 angular_range | — – 0.1100 Å−1 |
| 当前正则化参数 α current_alpha | 0.5729 |
| 最高正则化参数 α highest_alpha | 721900000.0000 |
| 实空间数据点数 n_real_points | 23 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.748; Stabil: 0.923; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.807 |
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) 60 domains
SCOP 2.08 (20 domains)
| 结构域编号 domain_id | d2df7a1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins) |
| 超家族 Superfamily superfamily | b.121.4 — Positive stranded ssRNA viruses |
| 家族 Family family | b.121.4.9 — Birnaviridae-like VP |
| 结构域编号 domain_id | d2df7b_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins) |
| 超家族 Superfamily superfamily | b.121.4 — Positive stranded ssRNA viruses |
| 家族 Family family | b.121.4.9 — Birnaviridae-like VP |
| 结构域编号 domain_id | d2df7c_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins) |
| 超家族 Superfamily superfamily | b.121.4 — Positive stranded ssRNA viruses |
| 家族 Family family | b.121.4.9 — Birnaviridae-like VP |
| 结构域编号 domain_id | d2df7d_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins) |
| 超家族 Superfamily superfamily | b.121.4 — Positive stranded ssRNA viruses |
| 家族 Family family | b.121.4.9 — Birnaviridae-like VP |
| 结构域编号 domain_id | d2df7e_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins) |
| 超家族 Superfamily superfamily | b.121.4 — Positive stranded ssRNA viruses |
| 家族 Family family | b.121.4.9 — Birnaviridae-like VP |
| 结构域编号 domain_id | d2df7f_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins) |
| 超家族 Superfamily superfamily | b.121.4 — Positive stranded ssRNA viruses |
| 家族 Family family | b.121.4.9 — Birnaviridae-like VP |
| 结构域编号 domain_id | d2df7g_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins) |
| 超家族 Superfamily superfamily | b.121.4 — Positive stranded ssRNA viruses |
| 家族 Family family | b.121.4.9 — Birnaviridae-like VP |
| 结构域编号 domain_id | d2df7h_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins) |
| 超家族 Superfamily superfamily | b.121.4 — Positive stranded ssRNA viruses |
| 家族 Family family | b.121.4.9 — Birnaviridae-like VP |
| 结构域编号 domain_id | d2df7i_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins) |
| 超家族 Superfamily superfamily | b.121.4 — Positive stranded ssRNA viruses |
| 家族 Family family | b.121.4.9 — Birnaviridae-like VP |
| 结构域编号 domain_id | d2df7j_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins) |
| 超家族 Superfamily superfamily | b.121.4 — Positive stranded ssRNA viruses |
| 家族 Family family | b.121.4.9 — Birnaviridae-like VP |
| 结构域编号 domain_id | d2df7k_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins) |
| 超家族 Superfamily superfamily | b.121.4 — Positive stranded ssRNA viruses |
| 家族 Family family | b.121.4.9 — Birnaviridae-like VP |
| 结构域编号 domain_id | d2df7l_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins) |
| 超家族 Superfamily superfamily | b.121.4 — Positive stranded ssRNA viruses |
| 家族 Family family | b.121.4.9 — Birnaviridae-like VP |
| 结构域编号 domain_id | d2df7m_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins) |
| 超家族 Superfamily superfamily | b.121.4 — Positive stranded ssRNA viruses |
| 家族 Family family | b.121.4.9 — Birnaviridae-like VP |
| 结构域编号 domain_id | d2df7n_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins) |
| 超家族 Superfamily superfamily | b.121.4 — Positive stranded ssRNA viruses |
| 家族 Family family | b.121.4.9 — Birnaviridae-like VP |
| 结构域编号 domain_id | d2df7o_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins) |
| 超家族 Superfamily superfamily | b.121.4 — Positive stranded ssRNA viruses |
| 家族 Family family | b.121.4.9 — Birnaviridae-like VP |
| 结构域编号 domain_id | d2df7p_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins) |
| 超家族 Superfamily superfamily | b.121.4 — Positive stranded ssRNA viruses |
| 家族 Family family | b.121.4.9 — Birnaviridae-like VP |
| 结构域编号 domain_id | d2df7q_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins) |
| 超家族 Superfamily superfamily | b.121.4 — Positive stranded ssRNA viruses |
| 家族 Family family | b.121.4.9 — Birnaviridae-like VP |
| 结构域编号 domain_id | d2df7r_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins) |
| 超家族 Superfamily superfamily | b.121.4 — Positive stranded ssRNA viruses |
| 家族 Family family | b.121.4.9 — Birnaviridae-like VP |
| 结构域编号 domain_id | d2df7s_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins) |
| 超家族 Superfamily superfamily | b.121.4 — Positive stranded ssRNA viruses |
| 家族 Family family | b.121.4.9 — Birnaviridae-like VP |
| 结构域编号 domain_id | d2df7t_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins) |
| 超家族 Superfamily superfamily | b.121.4 — Positive stranded ssRNA viruses |
| 家族 Family family | b.121.4.9 — Birnaviridae-like VP |
CATH v4.4 (40 domains)
| 结构域编号 domain_id | 2df7A01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2df7A02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 660 — icosahedral virus |
| 结构域编号 domain_id | 2df7B01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2df7B02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 660 — icosahedral virus |
| 结构域编号 domain_id | 2df7C01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2df7C02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 660 — icosahedral virus |
| 结构域编号 domain_id | 2df7D01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2df7D02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 660 — icosahedral virus |
| 结构域编号 domain_id | 2df7E01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2df7E02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 660 — icosahedral virus |
| 结构域编号 domain_id | 2df7F01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2df7F02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 660 — icosahedral virus |
| 结构域编号 domain_id | 2df7G01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2df7G02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 660 — icosahedral virus |
| 结构域编号 domain_id | 2df7H01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2df7H02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 660 — icosahedral virus |
| 结构域编号 domain_id | 2df7I01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2df7I02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 660 — icosahedral virus |
| 结构域编号 domain_id | 2df7J01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2df7J02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 660 — icosahedral virus |
| 结构域编号 domain_id | 2df7K01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2df7K02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 660 — icosahedral virus |
| 结构域编号 domain_id | 2df7L01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2df7L02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 660 — icosahedral virus |
| 结构域编号 domain_id | 2df7M01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2df7M02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 660 — icosahedral virus |
| 结构域编号 domain_id | 2df7N01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2df7N02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 660 — icosahedral virus |
| 结构域编号 domain_id | 2df7O01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2df7O02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 660 — icosahedral virus |
| 结构域编号 domain_id | 2df7P01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2df7P02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 660 — icosahedral virus |
| 结构域编号 domain_id | 2df7Q01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2df7Q02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 660 — icosahedral virus |
| 结构域编号 domain_id | 2df7R01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2df7R02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 660 — icosahedral virus |
| 结构域编号 domain_id | 2df7S01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2df7S02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 660 — icosahedral virus |
| 结构域编号 domain_id | 2df7T01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2df7T02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 120 — Jelly Rolls |
| 同源超家族 H-superfamily homologous superfamily | 660 — icosahedral virus |