2fdi
Crystal Structure of AlkB in complex with Fe(II), 2-oxoglutarate, and methylated trinucleotide T-meA-T (air 3 hours)
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 | 2fdi |
| 沉积日期 deposition_date | 2005-12-14 |
| 结构标题 title | Crystal Structure of AlkB in complex with Fe(II), 2-oxoglutarate, and methylated trinucleotide T-meA-T (air 3 hours) |
| 关键词 keywords | ;beta jellyroll, Structural Genomics, PSI, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, OXIDOREDUCTASE-DNA COMPLEX ;; OXIDOREDUCTASE/DNA |
| 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 | 16.70 Å |
| 回转半径 Rg (电子) rg_electron | 15.66 Å |
| 零角强度 I(0) i0 | 10411100.00 |
| 分子量 molecular_weight | 23207.0 kDa |
| 排除体积 excluded_volume | 28735 ų |
| 包络体积 envelope_volume | 31955 ų |
| 水化壳体积 shell_volume | 16609 ų |
| 包络直径 envelope_diameter | 50.8 Å |
| 壳层 Rg shell_rg | 22.27 Å |
| 包络 Rg envelope_rg | 16.02 Å |
| 形状 Rg shape_rg | 15.67 Å |
| 总 Rg total_rg | 16.72 Å |
| 总原子数 total_atoms | 1630 |
| 残基数 n_residues | 202 |
| 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 | 48.4 Å |
| Rg (实空间) rg_real | 16.52 Å |
| Rg 误差 (实空间) rg_real_error | 0.05 Å |
| I(0) (实空间) i0_real | 1.0030e+07 |
| I(0) 误差 (实空间) i0_real_error | 7.4140e+04 |
| Rg (倒空间) rg_reciprocal | 16.58 Å |
| I(0) (倒空间) i0_reciprocal | 10410000.0000 |
| 解质量估计 total_estimate | 0.7256 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 22.0 Å |
| 偏度 Skewness skewness | 0.063 |
| 峰度 Kurtosis kurtosis | -0.472 |
| 角度范围 angular_range | — – 0.4750 Å−1 |
| 当前正则化参数 α current_alpha | 12.0900 |
| 最高正则化参数 α highest_alpha | 3342000.0000 |
| 实空间数据点数 n_real_points | 78 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.953; Stabil: 0.916; Sysdev: 0.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.872 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (6)
6. 折叠分类 (SCOP + CATH) 2 domains
SCOP 2.08 (1 domains)
| 结构域编号 domain_id | d2fdia_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.82 — Double-stranded beta-helix |
| 超家族 Superfamily superfamily | b.82.2 — Clavaminate synthase-like |
| 家族 Family family | b.82.2.10 — AlkB-like |
CATH v4.4 (1 domains)
| 结构域编号 domain_id | 2fdiA00 |
| 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 | 590 — Alpha-ketoglutarate-dependent dioxygenase AlkB-like |