1uf2
The Atomic Structure of Rice dwarf Virus (RDV)
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 | 1uf2 |
| 沉积日期 deposition_date | 2003-05-23 |
| 结构标题 title | The Atomic Structure of Rice dwarf Virus (RDV) |
| 关键词 keywords | VIRUS COMPONENTS, Icosahedral virus, Virus; VIRUS |
| 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 | 66.35 Å |
| 回转半径 Rg (电子) rg_electron | 66.10 Å |
| 零角强度 I(0) i0 | 9131540000.00 |
| 分子量 molecular_weight | 825370.0 kDa |
| 排除体积 excluded_volume | 1038700 ų |
| 包络体积 envelope_volume | 1409200 ų |
| 水化壳体积 shell_volume | 173490 ų |
| 包络直径 envelope_diameter | 232.6 Å |
| 壳层 Rg shell_rg | 69.05 Å |
| 包络 Rg envelope_rg | 65.83 Å |
| 形状 Rg shape_rg | 66.10 Å |
| 总 Rg total_rg | 66.17 Å |
| 总原子数 total_atoms | 58130 |
| 残基数 n_residues | 7434 |
| 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 | 230.3 Å |
| Rg (实空间) rg_real | 66.28 Å |
| Rg 误差 (实空间) rg_real_error | 1.80 Å |
| I(0) (实空间) i0_real | 9.1320e+09 |
| I(0) 误差 (实空间) i0_real_error | 1.9760e+08 |
| Rg (倒空间) rg_reciprocal | 66.36 Å |
| I(0) (倒空间) i0_reciprocal | 9132000000.0000 |
| 解质量估计 total_estimate | 0.8675 |
| 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 | 76.8 Å |
| 偏度 Skewness skewness | 0.292 |
| 峰度 Kurtosis kurtosis | -0.488 |
| 角度范围 angular_range | — – 0.1200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0016 |
| 最高正则化参数 α highest_alpha | 2406000000.0000 |
| 实空间数据点数 n_real_points | 25 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.807 |
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) 41 domains
SCOP 2.08 (28 domains)
| 结构域编号 domain_id | d1uf2a_ |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.28 — Reovirus inner layer core protein p3 |
| 超家族 Superfamily superfamily | e.28.1 — Reovirus inner layer core protein p3 |
| 家族 Family family | e.28.1.2 — Phytoreovirus core |
| 结构域编号 domain_id | d1uf2b_ |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.28 — Reovirus inner layer core protein p3 |
| 超家族 Superfamily superfamily | e.28.1 — Reovirus inner layer core protein p3 |
| 家族 Family family | e.28.1.2 — Phytoreovirus core |
| 结构域编号 domain_id | d1uf2c1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.115 — A virus capsid protein alpha-helical domain |
| 超家族 Superfamily superfamily | a.115.1 — A virus capsid protein alpha-helical domain |
| 家族 Family family | a.115.1.3 — Phytoreovirus capsid |
| 结构域编号 domain_id | d1uf2c2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.19 — Viral protein domain |
| 超家族 Superfamily superfamily | b.19.1 — Viral protein domain |
| 家族 Family family | b.19.1.1 — Top domain of virus capsid protein |
| 结构域编号 domain_id | d1uf2d1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.115 — A virus capsid protein alpha-helical domain |
| 超家族 Superfamily superfamily | a.115.1 — A virus capsid protein alpha-helical domain |
| 家族 Family family | a.115.1.3 — Phytoreovirus capsid |
| 结构域编号 domain_id | d1uf2d2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.19 — Viral protein domain |
| 超家族 Superfamily superfamily | b.19.1 — Viral protein domain |
| 家族 Family family | b.19.1.1 — Top domain of virus capsid protein |
| 结构域编号 domain_id | d1uf2e1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.115 — A virus capsid protein alpha-helical domain |
| 超家族 Superfamily superfamily | a.115.1 — A virus capsid protein alpha-helical domain |
| 家族 Family family | a.115.1.3 — Phytoreovirus capsid |
| 结构域编号 domain_id | d1uf2e2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.19 — Viral protein domain |
| 超家族 Superfamily superfamily | b.19.1 — Viral protein domain |
| 家族 Family family | b.19.1.1 — Top domain of virus capsid protein |
| 结构域编号 domain_id | d1uf2f1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.115 — A virus capsid protein alpha-helical domain |
| 超家族 Superfamily superfamily | a.115.1 — A virus capsid protein alpha-helical domain |
| 家族 Family family | a.115.1.3 — Phytoreovirus capsid |
| 结构域编号 domain_id | d1uf2f2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.19 — Viral protein domain |
| 超家族 Superfamily superfamily | b.19.1 — Viral protein domain |
| 家族 Family family | b.19.1.1 — Top domain of virus capsid protein |
| 结构域编号 domain_id | d1uf2g1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.115 — A virus capsid protein alpha-helical domain |
| 超家族 Superfamily superfamily | a.115.1 — A virus capsid protein alpha-helical domain |
| 家族 Family family | a.115.1.3 — Phytoreovirus capsid |
| 结构域编号 domain_id | d1uf2g2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.19 — Viral protein domain |
| 超家族 Superfamily superfamily | b.19.1 — Viral protein domain |
| 家族 Family family | b.19.1.1 — Top domain of virus capsid protein |
| 结构域编号 domain_id | d1uf2h1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.115 — A virus capsid protein alpha-helical domain |
| 超家族 Superfamily superfamily | a.115.1 — A virus capsid protein alpha-helical domain |
| 家族 Family family | a.115.1.3 — Phytoreovirus capsid |
| 结构域编号 domain_id | d1uf2h2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.19 — Viral protein domain |
| 超家族 Superfamily superfamily | b.19.1 — Viral protein domain |
| 家族 Family family | b.19.1.1 — Top domain of virus capsid protein |
| 结构域编号 domain_id | d1uf2i1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.115 — A virus capsid protein alpha-helical domain |
| 超家族 Superfamily superfamily | a.115.1 — A virus capsid protein alpha-helical domain |
| 家族 Family family | a.115.1.3 — Phytoreovirus capsid |
| 结构域编号 domain_id | d1uf2i2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.19 — Viral protein domain |
| 超家族 Superfamily superfamily | b.19.1 — Viral protein domain |
| 家族 Family family | b.19.1.1 — Top domain of virus capsid protein |
| 结构域编号 domain_id | d1uf2j1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.115 — A virus capsid protein alpha-helical domain |
| 超家族 Superfamily superfamily | a.115.1 — A virus capsid protein alpha-helical domain |
| 家族 Family family | a.115.1.3 — Phytoreovirus capsid |
| 结构域编号 domain_id | d1uf2j2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.19 — Viral protein domain |
| 超家族 Superfamily superfamily | b.19.1 — Viral protein domain |
| 家族 Family family | b.19.1.1 — Top domain of virus capsid protein |
| 结构域编号 domain_id | d1uf2p1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.115 — A virus capsid protein alpha-helical domain |
| 超家族 Superfamily superfamily | a.115.1 — A virus capsid protein alpha-helical domain |
| 家族 Family family | a.115.1.3 — Phytoreovirus capsid |
| 结构域编号 domain_id | d1uf2p2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.19 — Viral protein domain |
| 超家族 Superfamily superfamily | b.19.1 — Viral protein domain |
| 家族 Family family | b.19.1.1 — Top domain of virus capsid protein |
| 结构域编号 domain_id | d1uf2q1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.115 — A virus capsid protein alpha-helical domain |
| 超家族 Superfamily superfamily | a.115.1 — A virus capsid protein alpha-helical domain |
| 家族 Family family | a.115.1.3 — Phytoreovirus capsid |
| 结构域编号 domain_id | d1uf2q2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.19 — Viral protein domain |
| 超家族 Superfamily superfamily | b.19.1 — Viral protein domain |
| 家族 Family family | b.19.1.1 — Top domain of virus capsid protein |
| 结构域编号 domain_id | d1uf2r1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.115 — A virus capsid protein alpha-helical domain |
| 超家族 Superfamily superfamily | a.115.1 — A virus capsid protein alpha-helical domain |
| 家族 Family family | a.115.1.3 — Phytoreovirus capsid |
| 结构域编号 domain_id | d1uf2r2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.19 — Viral protein domain |
| 超家族 Superfamily superfamily | b.19.1 — Viral protein domain |
| 家族 Family family | b.19.1.1 — Top domain of virus capsid protein |
| 结构域编号 domain_id | d1uf2s1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.115 — A virus capsid protein alpha-helical domain |
| 超家族 Superfamily superfamily | a.115.1 — A virus capsid protein alpha-helical domain |
| 家族 Family family | a.115.1.3 — Phytoreovirus capsid |
| 结构域编号 domain_id | d1uf2s2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.19 — Viral protein domain |
| 超家族 Superfamily superfamily | b.19.1 — Viral protein domain |
| 家族 Family family | b.19.1.1 — Top domain of virus capsid protein |
| 结构域编号 domain_id | d1uf2t1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.115 — A virus capsid protein alpha-helical domain |
| 超家族 Superfamily superfamily | a.115.1 — A virus capsid protein alpha-helical domain |
| 家族 Family family | a.115.1.3 — Phytoreovirus capsid |
| 结构域编号 domain_id | d1uf2t2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.19 — Viral protein domain |
| 超家族 Superfamily superfamily | b.19.1 — Viral protein domain |
| 家族 Family family | b.19.1.1 — Top domain of virus capsid protein |
CATH v4.4 (13 domains)
| 结构域编号 domain_id | 1uf2C02 |
| 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 | 170 — |
| 结构域编号 domain_id | 1uf2D02 |
| 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 | 170 — |
| 结构域编号 domain_id | 1uf2E02 |
| 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 | 170 — |
| 结构域编号 domain_id | 1uf2F02 |
| 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 | 170 — |
| 结构域编号 domain_id | 1uf2G02 |
| 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 | 170 — |
| 结构域编号 domain_id | 1uf2H02 |
| 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 | 170 — |
| 结构域编号 domain_id | 1uf2I02 |
| 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 | 170 — |
| 结构域编号 domain_id | 1uf2J02 |
| 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 | 170 — |
| 结构域编号 domain_id | 1uf2P02 |
| 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 | 170 — |
| 结构域编号 domain_id | 1uf2Q02 |
| 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 | 170 — |
| 结构域编号 domain_id | 1uf2R02 |
| 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 | 170 — |
| 结构域编号 domain_id | 1uf2S02 |
| 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 | 170 — |
| 结构域编号 domain_id | 1uf2T02 |
| 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 | 170 — |