1s0m
Crystal structure of a Benzo[a]pyrene Diol Epoxide adduct in a ternary complex with a 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 | 1s0m |
| 沉积日期 deposition_date | 2003-12-31 |
| 结构标题 title | Crystal structure of a Benzo[a]pyrene Diol Epoxide adduct in a ternary complex with a DNA polymerase |
| 关键词 keywords | Benzo pyrene, Carcinogen, LESION BYPASS, POLYMERASE, 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 | 35.86 Å |
| 回转半径 Rg (电子) rg_electron | 36.05 Å |
| 零角强度 I(0) i0 | 172542000.00 |
| 分子量 molecular_weight | 97653.0 kDa |
| 排除体积 excluded_volume | 118780 ų |
| 包络体积 envelope_volume | 161100 ų |
| 水化壳体积 shell_volume | 37727 ų |
| 包络直径 envelope_diameter | 120.1 Å |
| 壳层 Rg shell_rg | 41.92 Å |
| 包络 Rg envelope_rg | 35.24 Å |
| 形状 Rg shape_rg | 36.06 Å |
| 总 Rg total_rg | 36.38 Å |
| 总原子数 total_atoms | 6784 |
| 残基数 n_residues | 740 |
| 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 | 116.5 Å |
| Rg (实空间) rg_real | 35.98 Å |
| Rg 误差 (实空间) rg_real_error | 0.92 Å |
| I(0) (实空间) i0_real | 1.7250e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.0990e+06 |
| Rg (倒空间) rg_reciprocal | 35.91 Å |
| I(0) (倒空间) i0_reciprocal | 172500000.0000 |
| 解质量估计 total_estimate | 0.8766 |
| 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 | 34.4 Å |
| 偏度 Skewness skewness | 0.321 |
| 峰度 Kurtosis kurtosis | -0.699 |
| 角度范围 angular_range | — – 0.2200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 14470000.0000 |
| 实空间数据点数 n_real_points | 45 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.892; Smooth: 0.832 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (8)
6. 折叠分类 (SCOP + CATH) 12 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1s0ma1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.240 — Lesion bypass DNA polymerase (Y-family), little finger domain |
| 超家族 Superfamily superfamily | d.240.1 — Lesion bypass DNA polymerase (Y-family), little finger domain |
| 家族 Family family | d.240.1.1 — Lesion bypass DNA polymerase (Y-family), little finger domain |
| 结构域编号 domain_id | d1s0ma2 |
| 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.8.1.7 — Lesion bypass DNA polymerase (Y-family), catalytic domain |
| 结构域编号 domain_id | d1s0mb1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.240 — Lesion bypass DNA polymerase (Y-family), little finger domain |
| 超家族 Superfamily superfamily | d.240.1 — Lesion bypass DNA polymerase (Y-family), little finger domain |
| 家族 Family family | d.240.1.1 — Lesion bypass DNA polymerase (Y-family), little finger domain |
| 结构域编号 domain_id | d1s0mb2 |
| 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.8.1.7 — Lesion bypass DNA polymerase (Y-family), catalytic domain |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 1s0mA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1170 — MutS, DNA mismatch repair protein, domain I |
| 同源超家族 H-superfamily homologous superfamily | 60 — |
| 结构域编号 domain_id | 1s0mA02 |
| 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 | 270 — Reverse transcriptase/Diguanylate cyclase domain |
| 结构域编号 domain_id | 1s0mA03 |
| 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 | 1s0mA04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1490 — Dna Ligase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 100 — DNA polymerase, Y-family, little finger domain |
| 结构域编号 domain_id | 1s0mB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1170 — MutS, DNA mismatch repair protein, domain I |
| 同源超家族 H-superfamily homologous superfamily | 60 — |
| 结构域编号 domain_id | 1s0mB02 |
| 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 | 270 — Reverse transcriptase/Diguanylate cyclase domain |
| 结构域编号 domain_id | 1s0mB03 |
| 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 | 1s0mB04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1490 — Dna Ligase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 100 — DNA polymerase, Y-family, little finger domain |