2fz2
Structure of Turnip Yellow Mosaic Virus at 100 K
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 | 2fz2 |
| 沉积日期 deposition_date | 2006-02-08 |
| 结构标题 title | Structure of Turnip Yellow Mosaic Virus at 100 K |
| 关键词 keywords | Plant virus, Coat protein, Capsid protein, Tymoviruses, TYMV, RNA, Icosahedral virus, Virus-RNA COMPLEX; Virus/RNA |
| 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 | 29.74 Å |
| 回转半径 Rg (电子) rg_electron | 29.40 Å |
| 零角强度 I(0) i0 | 51719000.00 |
| 分子量 molecular_weight | 58768.0 kDa |
| 排除体积 excluded_volume | 74532 ų |
| 包络体积 envelope_volume | 95489 ų |
| 水化壳体积 shell_volume | 28017 ų |
| 包络直径 envelope_diameter | 98.7 Å |
| 壳层 Rg shell_rg | 35.16 Å |
| 包络 Rg envelope_rg | 29.57 Å |
| 形状 Rg shape_rg | 29.39 Å |
| 总 Rg total_rg | 30.01 Å |
| 总原子数 total_atoms | 4122 |
| 残基数 n_residues | 545 |
| 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 | 94.5 Å |
| Rg (实空间) rg_real | 29.76 Å |
| Rg 误差 (实空间) rg_real_error | 0.81 Å |
| I(0) (实空间) i0_real | 5.1720e+07 |
| I(0) 误差 (实空间) i0_real_error | 8.0120e+05 |
| Rg (倒空间) rg_reciprocal | 29.76 Å |
| I(0) (倒空间) i0_reciprocal | 51720000.0000 |
| 解质量估计 total_estimate | 0.9048 |
| 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 | 30.3 Å |
| 偏度 Skewness skewness | 0.238 |
| 峰度 Kurtosis kurtosis | -0.694 |
| 角度范围 angular_range | — – 0.2650 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 7117000.0000 |
| 实空间数据点数 n_real_points | 54 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.957; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.947; Smooth: 0.940 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (2)
6. 折叠分类 (SCOP + CATH) 6 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d2fz2a_ |
| 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.121.4.6 — Tymoviridae-like VP |
| 结构域编号 domain_id | d2fz2b_ |
| 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.121.4.6 — Tymoviridae-like VP |
| 结构域编号 domain_id | d2fz2c_ |
| 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.121.4.6 — Tymoviridae-like VP |
CATH v4.4 (3 domains)
| 结构域编号 domain_id | 2fz2A00 |
| 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 | 2fz2B00 |
| 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 | 2fz2C00 |
| 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 — |