2bdp
CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I FRAGMENT COMPLEXED TO 9 BASE PAIRS OF DUPLEX DNA
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 | 2bdp |
| 沉积日期 deposition_date | 1997-11-17 |
| 结构标题 title | CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I FRAGMENT COMPLEXED TO 9 BASE PAIRS OF DUPLEX DNA |
| 关键词 keywords | ;BACILLUS STEAROTHERMOPHILUS DNA POLYMERASE, BF THERMOPHILUS POLYMERASE, COMPLEX (NUCLEOTIDYLTRANSFERASE-DNA), 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 | 26.97 Å |
| 回转半径 Rg (电子) rg_electron | 26.29 Å |
| 零角强度 I(0) i0 | 92230200.00 |
| 分子量 molecular_weight | 72242.0 kDa |
| 排除体积 excluded_volume | 89096 ų |
| 包络体积 envelope_volume | 108790 ų |
| 水化壳体积 shell_volume | 34090 ų |
| 包络直径 envelope_diameter | 88.6 Å |
| 壳层 Rg shell_rg | 34.06 Å |
| 包络 Rg envelope_rg | 26.23 Å |
| 形状 Rg shape_rg | 26.30 Å |
| 总 Rg total_rg | 27.01 Å |
| 总原子数 total_atoms | 5059 |
| 残基数 n_residues | 599 |
| 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 | 86.2 Å |
| Rg (实空间) rg_real | 26.85 Å |
| Rg 误差 (实空间) rg_real_error | 0.41 Å |
| I(0) (实空间) i0_real | 9.2230e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.1350e+06 |
| Rg (倒空间) rg_reciprocal | 26.89 Å |
| I(0) (倒空间) i0_reciprocal | 92230000.0000 |
| 解质量估计 total_estimate | 0.8940 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 32.1 Å |
| 偏度 Skewness skewness | 0.230 |
| 峰度 Kurtosis kurtosis | -0.360 |
| 角度范围 angular_range | — – 0.2950 Å−1 |
| 当前正则化参数 α current_alpha | 0.0001 |
| 最高正则化参数 α highest_alpha | 19720000.0000 |
| 实空间数据点数 n_real_points | 60 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.958 |
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) 6 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d2bdpa1 |
| 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.55.3.5 — DnaQ-like 3'-5' exonuclease |
| 结构域编号 domain_id | d2bdpa2 |
| 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.8.1.1 — DNA polymerase I |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 2bdpA01 |
| 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 | 2bdpA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1060 — Taq DNA Polymerase; Chain T, domain 4 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Taq DNA Polymerase; Chain T, domain 4 |
| 结构域编号 domain_id | 2bdpA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 370 — |
| 结构域编号 domain_id | 2bdpA04 |
| 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 |