1wth
Crystal structure of gp5-S351L mutant and gp27 complex
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 | 1wth |
| 沉积日期 deposition_date | 2004-11-23 |
| 结构标题 title | Crystal structure of gp5-S351L mutant and gp27 complex |
| 关键词 keywords | Triple-stranded beta-helix, OB fold, pseudohexamer, T4 tail lysozyme, HUB, gp5-gp27, Hydrolase-Structural protein COMPLEX; Hydrolase/Structural 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 | 48.73 Å |
| 回转半径 Rg (电子) rg_electron | 50.34 Å |
| 零角强度 I(0) i0 | 167562000.00 |
| 分子量 molecular_weight | 103860.0 kDa |
| 排除体积 excluded_volume | 129160 ų |
| 包络体积 envelope_volume | 217350 ų |
| 水化壳体积 shell_volume | 39677 ų |
| 包络直径 envelope_diameter | 201.2 Å |
| 壳层 Rg shell_rg | 45.22 Å |
| 包络 Rg envelope_rg | 53.55 Å |
| 形状 Rg shape_rg | 50.31 Å |
| 总 Rg total_rg | 50.19 Å |
| 总原子数 total_atoms | 7297 |
| 残基数 n_residues | 932 |
| 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 | 189.3 Å |
| Rg (实空间) rg_real | 50.09 Å |
| Rg 误差 (实空间) rg_real_error | 3.81 Å |
| I(0) (实空间) i0_real | 1.6760e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.5530e+06 |
| Rg (倒空间) rg_reciprocal | 48.74 Å |
| I(0) (倒空间) i0_reciprocal | 167300000.0000 |
| 解质量估计 total_estimate | 0.6606 |
| 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 | 35.5 Å |
| 偏度 Skewness skewness | 0.717 |
| 峰度 Kurtosis kurtosis | -0.031 |
| 角度范围 angular_range | — – 0.1600 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 11650000.0000 |
| 实空间数据点数 n_real_points | 33 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.264; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.119; Smooth: 0.674 |
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) 9 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d1wthd1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.106 — Phage tail proteins |
| 超家族 Superfamily superfamily | b.106.1 — Phage tail proteins |
| 家族 Family family | b.106.1.1 — Baseplate protein-like |
| 结构域编号 domain_id | d1wthd2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.106 — Phage tail proteins |
| 超家族 Superfamily superfamily | b.106.1 — Phage tail proteins |
| 家族 Family family | b.106.1.1 — Baseplate protein-like |
CATH v4.4 (7 domains)
| 结构域编号 domain_id | 1wthA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P) |
| 同源超家族 H-superfamily homologous superfamily | 260 — Nucleic acid-binding protein domain |
| 结构域编号 domain_id | 1wthA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 450 — Nuclear Transport Factor 2; Chain: A, |
| 同源超家族 H-superfamily homologous superfamily | 190 — |
| 结构域编号 domain_id | 1wthA03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 530 — Lysozyme |
| 同源超家族 H-superfamily homologous superfamily | 40 — |
| 结构域编号 domain_id | 1wthD01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 10 — Thrombin, subunit H |
| 同源超家族 H-superfamily homologous superfamily | 10 — Trypsin-like serine proteases |
| 结构域编号 domain_id | 1wthD02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 55 — 3-Layer(bab) Sandwich |
| 拓扑 Topology topology | 50 — Phage tail protein beta-alpha-beta fold |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1wthD03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 30 — Elongation Factor Tu (Ef-tu); domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 150 — Bacteriophage T4, Gp27, baseplate hub, domain 3 |
| 结构域编号 domain_id | 1wthD04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1920 — Phage tail proteins - 2 layer sandwich fold |
| 同源超家族 H-superfamily homologous superfamily | 40 — |