1pqk
Repacking of the Core of T4 Lysozyme by Automated Design
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 | 1pqk |
| 沉积日期 deposition_date | 2003-06-18 |
| 结构标题 title | Repacking of the Core of T4 Lysozyme by Automated Design |
| 关键词 keywords | ;HYDROLASE (O-GLYCOSYL), T4 LYSOZYME, DESIGNED CORE MUTANT, AUTOMATED PROTEIN DESIGN, PROTEIN ENGINEERING, PROTEIN FOLDING, PROTEIN STABILITY, CORE REPACKING, BACK REVERTANT, DEAD-END ELIMINATION THEOREM, SIDE-CHAIN PACKING, OPTIMIZED ROTAMER COMBINATIONS, ORBIT, HYDROLASE ;; HYDROLASE |
| 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 | 27.09 Å |
| 回转半径 Rg (电子) rg_electron | 26.35 Å |
| 零角强度 I(0) i0 | 51371400.00 |
| 分子量 molecular_weight | 56017.0 kDa |
| 排除体积 excluded_volume | 70357 ų |
| 包络体积 envelope_volume | 84433 ų |
| 水化壳体积 shell_volume | 27672 ų |
| 包络直径 envelope_diameter | 91.5 Å |
| 壳层 Rg shell_rg | 32.56 Å |
| 包络 Rg envelope_rg | 26.22 Å |
| 形状 Rg shape_rg | 26.34 Å |
| 总 Rg total_rg | 27.04 Å |
| 总原子数 total_atoms | 3948 |
| 残基数 n_residues | 492 |
| 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 | 90.2 Å |
| Rg (实空间) rg_real | 27.14 Å |
| Rg 误差 (实空间) rg_real_error | 0.63 Å |
| I(0) (实空间) i0_real | 5.1370e+07 |
| I(0) 误差 (实空间) i0_real_error | 6.8750e+05 |
| Rg (倒空间) rg_reciprocal | 27.13 Å |
| I(0) (倒空间) i0_reciprocal | 51370000.0000 |
| 解质量估计 total_estimate | 0.6708 |
| 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 | 32.1 Å |
| 偏度 Skewness skewness | 0.385 |
| 峰度 Kurtosis kurtosis | -0.315 |
| 角度范围 angular_range | — – 0.2950 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 11360000.0000 |
| 实空间数据点数 n_real_points | 60 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 0.089; Positv: 1.000; Valcen: 0.936; Smooth: 0.883 |
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 | d1pqka_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.2 — Lysozyme-like |
| 超家族 Superfamily superfamily | d.2.1 — Lysozyme-like |
| 家族 Family family | d.2.1.3 — Phage lysozyme |
| 结构域编号 domain_id | d1pqkb_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.2 — Lysozyme-like |
| 超家族 Superfamily superfamily | d.2.1 — Lysozyme-like |
| 家族 Family family | d.2.1.3 — Phage lysozyme |
| 结构域编号 domain_id | d1pqkc_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.2 — Lysozyme-like |
| 超家族 Superfamily superfamily | d.2.1 — Lysozyme-like |
| 家族 Family family | d.2.1.3 — Phage lysozyme |
CATH v4.4 (3 domains)
| 结构域编号 domain_id | 1pqkA00 |
| 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 | 1pqkB00 |
| 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 | 1pqkC00 |
| 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 — |