2cfm
ATP-DEPENDENT DNA LIGASE FROM PYROCOCCUS FURIOSUS
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 | 2cfm |
| 沉积日期 deposition_date | 2006-02-22 |
| 结构标题 title | ATP-DEPENDENT DNA LIGASE FROM PYROCOCCUS FURIOSUS |
| 关键词 keywords | ;LIGASE, PROTEIN-NUCLEOTIDE COMPLEX, CELL CYCLE, CELL DIVISION, DNA DAMAGE, DNA RECOMBINATION, DNA REPAIR, DNA REPLICATION, NUCLEOTIDE-BINDING ;; LIGASE |
| 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 | 25.90 Å |
| 回转半径 Rg (电子) rg_electron | 24.95 Å |
| 零角强度 I(0) i0 | 64041100.00 |
| 分子量 molecular_weight | 63935.0 kDa |
| 排除体积 excluded_volume | 80491 ų |
| 包络体积 envelope_volume | 94127 ų |
| 水化壳体积 shell_volume | 31101 ų |
| 包络直径 envelope_diameter | 92.5 Å |
| 壳层 Rg shell_rg | 32.38 Å |
| 包络 Rg envelope_rg | 25.05 Å |
| 形状 Rg shape_rg | 24.92 Å |
| 总 Rg total_rg | 25.83 Å |
| 总原子数 total_atoms | 4447 |
| 残基数 n_residues | 545 |
| 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 | 88.8 Å |
| Rg (实空间) rg_real | 25.81 Å |
| Rg 误差 (实空间) rg_real_error | 0.59 Å |
| I(0) (实空间) i0_real | 6.4040e+07 |
| I(0) 误差 (实空间) i0_real_error | 9.3060e+05 |
| Rg (倒空间) rg_reciprocal | 25.84 Å |
| I(0) (倒空间) i0_reciprocal | 64040000.0000 |
| 解质量估计 total_estimate | 0.6651 |
| 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 | 87.3 Å |
| 偏度 Skewness skewness | 0.256 |
| 峰度 Kurtosis kurtosis | -0.284 |
| 角度范围 angular_range | — – 0.3050 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 15640000.0000 |
| 实空间数据点数 n_real_points | 62 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.786; Stabil: 1.000; Sysdev: 0.105; Positv: 1.000; Valcen: 0.997; Smooth: 0.972 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (4)
6. 折叠分类 (SCOP + CATH) 3 domains
CATH v4.4 (3 domains)
| 结构域编号 domain_id | 2cfmA01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3260 — DNA ligase i, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — DNA ligase, ATP-dependent, N-terminal domain |
| 结构域编号 domain_id | 2cfmA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 470 — D-amino Acid Aminotransferase; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 30 — DNA ligase/mRNA capping enzyme |
| 结构域编号 domain_id | 2cfmA03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P) |
| 同源超家族 H-superfamily homologous superfamily | 140 — Nucleic acid-binding proteins |