1huz
CRYSTAL STRUCTURE OF DNA POLYMERASE COMPLEXED WITH DNA AND CR-PCP
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 | 1huz |
| 沉积日期 deposition_date | 2001-01-04 |
| 结构标题 title | CRYSTAL STRUCTURE OF DNA POLYMERASE COMPLEXED WITH DNA AND CR-PCP |
| 关键词 keywords | PROTEIN-DNA COMPLEX, 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 | 42.86 Å |
| 回转半径 Rg (电子) rg_electron | 43.25 Å |
| 零角强度 I(0) i0 | 125245000.00 |
| 分子量 molecular_weight | 84175.0 kDa |
| 排除体积 excluded_volume | 102270 ų |
| 包络体积 envelope_volume | 159120 ų |
| 水化壳体积 shell_volume | 31033 ų |
| 包络直径 envelope_diameter | 136.1 Å |
| 壳层 Rg shell_rg | 48.12 Å |
| 包络 Rg envelope_rg | 41.67 Å |
| 形状 Rg shape_rg | 43.26 Å |
| 总 Rg total_rg | 43.45 Å |
| 总原子数 total_atoms | 5872 |
| 残基数 n_residues | 682 |
| 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 | 126.3 Å |
| Rg (实空间) rg_real | 43.22 Å |
| Rg 误差 (实空间) rg_real_error | 1.16 Å |
| I(0) (实空间) i0_real | 1.2520e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.1030e+06 |
| Rg (倒空间) rg_reciprocal | 42.87 Å |
| I(0) (倒空间) i0_reciprocal | 125200000.0000 |
| 解质量估计 total_estimate | 0.6595 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 3 |
| 主峰位置 r_peak_primary | 27.3 Å |
| 偏度 Skewness skewness | 0.273 |
| 峰度 Kurtosis kurtosis | -1.114 |
| 角度范围 angular_range | — – 0.1850 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 9990000.0000 |
| 实空间数据点数 n_real_points | 38 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.395; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.384; Smooth: 0.001 |
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) 14 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1huza1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.60 — SAM domain-like |
| 超家族 Superfamily superfamily | a.60.6 — DNA polymerase beta, N-terminal domain-like |
| 家族 Family family | a.60.6.1 — DNA polymerase beta, N-terminal domain-like |
| 结构域编号 domain_id | d1huza3 |
| 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 | d1huza4 |
| 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 |
| 结构域编号 domain_id | d1huzb1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.60 — SAM domain-like |
| 超家族 Superfamily superfamily | a.60.6 — DNA polymerase beta, N-terminal domain-like |
| 家族 Family family | a.60.6.1 — DNA polymerase beta, N-terminal domain-like |
| 结构域编号 domain_id | d1huzb3 |
| 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 | d1huzb4 |
| 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 (8 domains)
| 结构域编号 domain_id | 1huzA01 |
| 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 | 110 — DNA polymerase beta, N-terminal domain-like |
| 结构域编号 domain_id | 1huzA02 |
| 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 | 1huzA03 |
| 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 | 1huzA04 |
| 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 |
| 结构域编号 domain_id | 1huzB01 |
| 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 | 110 — DNA polymerase beta, N-terminal domain-like |
| 结构域编号 domain_id | 1huzB02 |
| 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 | 1huzB03 |
| 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 | 1huzB04 |
| 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 |