2dqb
Crystal structure of dNTP triphosphohydrolase from Thermus thermophilus HB8, which is homologous to dGTP triphosphohydrolase
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 | 2dqb |
| 沉积日期 deposition_date | 2006-05-25 |
| 结构标题 title | Crystal structure of dNTP triphosphohydrolase from Thermus thermophilus HB8, which is homologous to dGTP triphosphohydrolase |
| 关键词 keywords | ;dNTPase, dNTP, triphosphohydrolase, single-stranded DNA, DNA, dGTPase, HD superfamily, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, HYDROLASE, DNA BINDING PROTEIN ;; HYDROLASE, DNA BINDING PROTEIN |
| 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 | 43.11 Å |
| 回转半径 Rg (电子) rg_electron | 42.38 Å |
| 零角强度 I(0) i0 | 919304000.00 |
| 分子量 molecular_weight | 245230.0 kDa |
| 排除体积 excluded_volume | 304960 ų |
| 包络体积 envelope_volume | 400200 ų |
| 水化壳体积 shell_volume | 77498 ų |
| 包络直径 envelope_diameter | 131.5 Å |
| 壳层 Rg shell_rg | 48.78 Å |
| 包络 Rg envelope_rg | 41.21 Å |
| 形状 Rg shape_rg | 42.36 Å |
| 总 Rg total_rg | 42.72 Å |
| 总原子数 total_atoms | 17241 |
| 残基数 n_residues | 2136 |
| 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 | 128.3 Å |
| Rg (实空间) rg_real | 42.92 Å |
| Rg 误差 (实空间) rg_real_error | 0.76 Å |
| I(0) (实空间) i0_real | 9.1930e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.5240e+07 |
| Rg (倒空间) rg_reciprocal | 43.11 Å |
| I(0) (倒空间) i0_reciprocal | 919500000.0000 |
| 解质量估计 total_estimate | 0.8847 |
| 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 | 48.5 Å |
| 偏度 Skewness skewness | 0.104 |
| 峰度 Kurtosis kurtosis | -0.715 |
| 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 | 212100000.0000 |
| 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: 0.982; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.556 |
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
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 2dqbA00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3210 — Hypothetical protein af1432 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Hypothetical protein af1432 |
| 结构域编号 domain_id | 2dqbB00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3210 — Hypothetical protein af1432 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Hypothetical protein af1432 |
| 结构域编号 domain_id | 2dqbC00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3210 — Hypothetical protein af1432 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Hypothetical protein af1432 |
| 结构域编号 domain_id | 2dqbD00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3210 — Hypothetical protein af1432 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Hypothetical protein af1432 |
| 结构域编号 domain_id | 2dqbE00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3210 — Hypothetical protein af1432 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Hypothetical protein af1432 |
| 结构域编号 domain_id | 2dqbF00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3210 — Hypothetical protein af1432 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Hypothetical protein af1432 |