2i9k
Engineered Extrahelical Base Destabilization Enhances Sequence Discrimination of DNA Methyltransferase M.HhaI
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 | 2i9k |
| 沉积日期 deposition_date | 2006-09-05 |
| 结构标题 title | Engineered Extrahelical Base Destabilization Enhances Sequence Discrimination of DNA Methyltransferase M.HhaI |
| 关键词 keywords | Phe124Ala mutation in M.HhaI, TRANSFERASE-DNA COMPLEX; TRANSFERASE/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 | 21.54 Å |
| 回转半径 Rg (电子) rg_electron | 20.55 Å |
| 零角强度 I(0) i0 | 40475600.00 |
| 分子量 molecular_weight | 44729.0 kDa |
| 排除体积 excluded_volume | 53929 ų |
| 包络体积 envelope_volume | 61630 ų |
| 水化壳体积 shell_volume | 24392 ų |
| 包络直径 envelope_diameter | 79.6 Å |
| 壳层 Rg shell_rg | 27.95 Å |
| 包络 Rg envelope_rg | 21.06 Å |
| 形状 Rg shape_rg | 20.52 Å |
| 总 Rg total_rg | 21.42 Å |
| 总原子数 total_atoms | 3119 |
| 残基数 n_residues | 352 |
| 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 | 73.2 Å |
| Rg (实空间) rg_real | 21.44 Å |
| Rg 误差 (实空间) rg_real_error | 0.51 Å |
| I(0) (实空间) i0_real | 4.0480e+07 |
| I(0) 误差 (实空间) i0_real_error | 4.9200e+05 |
| Rg (倒空间) rg_reciprocal | 21.46 Å |
| I(0) (倒空间) i0_reciprocal | 40480000.0000 |
| 解质量估计 total_estimate | 0.7925 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 3 |
| 主峰位置 r_peak_primary | 26.9 Å |
| 偏度 Skewness skewness | 0.259 |
| 峰度 Kurtosis kurtosis | -0.294 |
| 角度范围 angular_range | — – 0.3700 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 7171000.0000 |
| 实空间数据点数 n_real_points | 69 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.768; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (3)
6. 折叠分类 (SCOP + CATH) 3 domains
SCOP 2.08 (1 domains)
| 结构域编号 domain_id | d2i9ka_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.66 — S-adenosyl-L-methionine-dependent methyltransferases |
| 超家族 Superfamily superfamily | c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases |
| 家族 Family family | c.66.1.26 — C5 cytosine-specific DNA methylase, DCM |
CATH v4.4 (2 domains)
| 结构域编号 domain_id | 2i9kA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 150 — Vaccinia Virus protein VP39 |
| 结构域编号 domain_id | 2i9kA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 120 — DNA Methylase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — DNA Methylase, subunit A, domain 2 |