9mrv
Crystal structures of a cyanobacterial DAP epimerase bound to D,L-alpha-methyl DAP
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 | 9mrv |
| 沉积日期 deposition_date | 2025-01-08 |
| 最后修订 last_revision | 2025-07-16 |
| 结构标题 title | Crystal structures of a cyanobacterial DAP epimerase bound to D,L-alpha-methyl DAP |
| 关键词 keywords | ;DAP epimerase, diaminopimelic acid, DapF, cofactor-independent, protein biochemistry, enzyme mechanism, inhibitor, antibiotic, lysine biosynthesis ;; ANTIBIOTIC |
| 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 | 40.65 Å |
| 回转半径 Rg (电子) rg_electron | 40.11 Å |
| 零角强度 I(0) i0 | 226648000.00 |
| 分子量 molecular_weight | 122000.0 kDa |
| 排除体积 excluded_volume | 152250 ų |
| 包络体积 envelope_volume | 209570 ų |
| 水化壳体积 shell_volume | 42550 ų |
| 包络直径 envelope_diameter | 122.9 Å |
| 壳层 Rg shell_rg | 47.50 Å |
| 包络 Rg envelope_rg | 38.75 Å |
| 形状 Rg shape_rg | 40.13 Å |
| 总 Rg total_rg | 40.44 Å |
| 总原子数 total_atoms | 17040 |
| 残基数 n_residues | 1116 |
| 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 | 121.0 Å |
| Rg (实空间) rg_real | 40.47 Å |
| Rg 误差 (实空间) rg_real_error | 1.12 Å |
| I(0) (实空间) i0_real | 2.2660e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.9980e+06 |
| Rg (倒空间) rg_reciprocal | 40.65 Å |
| I(0) (倒空间) i0_reciprocal | 226700000.0000 |
| 解质量估计 total_estimate | 0.8678 |
| 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 | 62.0 Å |
| 偏度 Skewness skewness | -0.114 |
| 峰度 Kurtosis kurtosis | -0.869 |
| 角度范围 angular_range | — – 0.1950 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 17820000.0000 |
| 实空间数据点数 n_real_points | 40 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.799; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.898 |