2jgu
crystal structure of DNA-directed DNA polymerase
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 | 2jgu |
| 沉积日期 deposition_date | 2007-02-15 |
| 结构标题 title | crystal structure of DNA-directed DNA polymerase |
| 关键词 keywords | ;DNA-DIRECTED DNA POLYMERASE, PFU, NUCLEASE, HYDROLASE, TRANSFERASE, DNA-BINDING, ENDONUCLEASE, DNA REPLICATION, NUCLEOTIDYLTRANSFERASE ;; TRANSFERASE |
| 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 | 31.80 Å |
| 回转半径 Rg (电子) rg_electron | 30.91 Å |
| 零角强度 I(0) i0 | 98426600.00 |
| 分子量 molecular_weight | 82538.0 kDa |
| 排除体积 excluded_volume | 105210 ų |
| 包络体积 envelope_volume | 142240 ų |
| 水化壳体积 shell_volume | 38431 ų |
| 包络直径 envelope_diameter | 103.4 Å |
| 壳层 Rg shell_rg | 38.04 Å |
| 包络 Rg envelope_rg | 30.33 Å |
| 形状 Rg shape_rg | 30.90 Å |
| 总 Rg total_rg | 31.67 Å |
| 总原子数 total_atoms | 5828 |
| 残基数 n_residues | 712 |
| 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 | 98.6 Å |
| Rg (实空间) rg_real | 31.66 Å |
| Rg 误差 (实空间) rg_real_error | 0.88 Å |
| I(0) (实空间) i0_real | 9.8430e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.7830e+06 |
| Rg (倒空间) rg_reciprocal | 31.72 Å |
| I(0) (倒空间) i0_reciprocal | 98430000.0000 |
| 解质量估计 total_estimate | 0.6930 |
| 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 | 94.7 Å |
| 偏度 Skewness skewness | 0.124 |
| 峰度 Kurtosis kurtosis | -0.616 |
| 角度范围 angular_range | — – 0.2500 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 20400000.0000 |
| 实空间数据点数 n_real_points | 51 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.958; Stabil: 0.999; Sysdev: 0.062; Positv: 1.000; Valcen: 0.999; Smooth: 0.949 |
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) 6 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d2jgua1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.55 — Ribonuclease H-like motif |
| 超家族 Superfamily superfamily | c.55.3 — Ribonuclease H-like |
| 家族 Family family | c.55.3.0 — automated matches |
| 结构域编号 domain_id | d2jgua2 |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.8 — DNA/RNA polymerases |
| 超家族 Superfamily superfamily | e.8.1 — DNA/RNA polymerases |
| 家族 Family family | e.8.1.0 — automated matches |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 2jguA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 342 — DNA Polymerase; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — DNA Polymerase, chain B, domain 1 |
| 结构域编号 domain_id | 2jguA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 420 — Nucleotidyltransferase; domain 5 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ribonuclease H-like superfamily/Ribonuclease H |
| 结构域编号 domain_id | 2jguA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1600 — Palm domain of DNA polymerase |
| 同源超家族 H-superfamily homologous superfamily | 10 — B family DNA polymerase, palm domain |
| 结构域编号 domain_id | 2jguA04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 287 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 690 — B family DNA polymerase, finger domain |