1nom
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF MNCL2 (5 MILLIMOLAR)
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 | 1nom |
| 沉积日期 deposition_date | 1996-04-19 |
| 结构标题 title | DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF MNCL2 (5 MILLIMOLAR) |
| 关键词 keywords | DNA-DIRECTED DNA POLYMERASE, DNA REPLICATION, DNA REPAIR, NUCLEOTIDYLTRANSFERASE; NUCLEOTIDYLTRANSFERASE |
| 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 | 21.17 Å |
| 回转半径 Rg (电子) rg_electron | 20.27 Å |
| 零角强度 I(0) i0 | 13660300.00 |
| 分子量 molecular_weight | 27414.0 kDa |
| 排除体积 excluded_volume | 34105 ų |
| 包络体积 envelope_volume | 41348 ų |
| 水化壳体积 shell_volume | 17633 ų |
| 包络直径 envelope_diameter | 68.8 Å |
| 壳层 Rg shell_rg | 26.11 Å |
| 包络 Rg envelope_rg | 20.46 Å |
| 形状 Rg shape_rg | 20.30 Å |
| 总 Rg total_rg | 20.97 Å |
| 总原子数 total_atoms | 1929 |
| 残基数 n_residues | 242 |
| 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 | 66.8 Å |
| Rg (实空间) rg_real | 21.14 Å |
| Rg 误差 (实空间) rg_real_error | 0.44 Å |
| I(0) (实空间) i0_real | 1.3660e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.7960e+05 |
| Rg (倒空间) rg_reciprocal | 21.15 Å |
| I(0) (倒空间) i0_reciprocal | 13660000.0000 |
| 解质量估计 total_estimate | 0.9071 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 64.8 Å |
| 偏度 Skewness skewness | 0.243 |
| 峰度 Kurtosis kurtosis | -0.561 |
| 角度范围 angular_range | — – 0.3750 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 4162000.0000 |
| 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: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.998 |
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) 5 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d1noma1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.60 — SAM domain-like |
| 超家族 Superfamily superfamily | a.60.12 — PsbU/PolX domain-like |
| 家族 Family family | a.60.12.1 — DNA polymerase beta-like, second domain |
| 结构域编号 domain_id | d1noma2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.218 — Nucleotidyltransferase |
| 超家族 Superfamily superfamily | d.218.1 — Nucleotidyltransferase |
| 家族 Family family | d.218.1.2 — DNA polymerase beta-like |
CATH v4.4 (3 domains)
| 结构域编号 domain_id | 1nomA01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 150 — DNA polymerase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — 5' to 3' exonuclease, C-terminal subdomain |
| 结构域编号 domain_id | 1nomA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 460 — Beta Polymerase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Beta Polymerase, domain 2 |
| 结构域编号 domain_id | 1nomA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 210 — Beta Polymerase; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — DNA polymerase, thumb domain |