1nj4
Crystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 1.9 A resolution
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 | 1nj4 |
| 沉积日期 deposition_date | 2002-12-30 |
| 结构标题 title | Crystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 1.9 A resolution |
| 关键词 keywords | peptidoglycan synthesis, penicllin-binding protein, DD-carboxypeptidase, 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 | 24.17 Å |
| 回转半径 Rg (电子) rg_electron | 23.62 Å |
| 零角强度 I(0) i0 | 24313200.00 |
| 分子量 molecular_weight | 37693.0 kDa |
| 排除体积 excluded_volume | 47224 ų |
| 包络体积 envelope_volume | 57595 ų |
| 水化壳体积 shell_volume | 21443 ų |
| 包络直径 envelope_diameter | 88.1 Å |
| 壳层 Rg shell_rg | 29.30 Å |
| 包络 Rg envelope_rg | 24.05 Å |
| 形状 Rg shape_rg | 23.65 Å |
| 总 Rg total_rg | 24.22 Å |
| 总原子数 total_atoms | 2649 |
| 残基数 n_residues | 343 |
| 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 | 84.6 Å |
| Rg (实空间) rg_real | 24.30 Å |
| Rg 误差 (实空间) rg_real_error | 0.65 Å |
| I(0) (实空间) i0_real | 2.4310e+07 |
| I(0) 误差 (实空间) i0_real_error | 3.4070e+05 |
| Rg (倒空间) rg_reciprocal | 24.27 Å |
| I(0) (倒空间) i0_reciprocal | 24310000.0000 |
| 解质量估计 total_estimate | 0.7752 |
| 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 | 23.8 Å |
| 偏度 Skewness skewness | 0.465 |
| 峰度 Kurtosis kurtosis | -0.328 |
| 角度范围 angular_range | — – 0.3300 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 6065000.0000 |
| 实空间数据点数 n_real_points | 65 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.760; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.795; Smooth: 0.000 |
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) 4 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d1nj4a1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.105 — Penicillin-binding protein associated domain |
| 超家族 Superfamily superfamily | b.105.1 — Penicillin-binding protein associated domain |
| 家族 Family family | b.105.1.1 — PBP5 C-terminal domain-like |
| 结构域编号 domain_id | d1nj4a2 |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.3 — beta-lactamase/transpeptidase-like |
| 超家族 Superfamily superfamily | e.3.1 — beta-lactamase/transpeptidase-like |
| 家族 Family family | e.3.1.1 — beta-Lactamase/D-ala carboxypeptidase |
CATH v4.4 (2 domains)
| 结构域编号 domain_id | 1nj4A01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 710 — Beta-lactamase |
| 同源超家族 H-superfamily homologous superfamily | 10 — DD-peptidase/beta-lactamase superfamily |
| 结构域编号 domain_id | 1nj4A02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 410 — Peptidoglycan synthesis regulatory factor (PBP3), Domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — D-Ala-D-Ala carboxypeptidase, C-terminal domain |