1it7
Crystal structure of archaeosine tRNA-guanine transglycosylase complexed with guanine
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 | 1it7 |
| 沉积日期 deposition_date | 2002-01-11 |
| 结构标题 title | Crystal structure of archaeosine tRNA-guanine transglycosylase complexed with guanine |
| 关键词 keywords | (ALPHA/BETA)8 BARREL, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, TRANSFERASE; 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 | 34.13 Å |
| 回转半径 Rg (电子) rg_electron | 33.37 Å |
| 零角强度 I(0) i0 | 257714000.00 |
| 分子量 molecular_weight | 132440.0 kDa |
| 排除体积 excluded_volume | 167230 ų |
| 包络体积 envelope_volume | 199700 ų |
| 水化壳体积 shell_volume | 49177 ų |
| 包络直径 envelope_diameter | 110.3 Å |
| 壳层 Rg shell_rg | 40.76 Å |
| 包络 Rg envelope_rg | 33.40 Å |
| 形状 Rg shape_rg | 33.35 Å |
| 总 Rg total_rg | 33.96 Å |
| 总原子数 total_atoms | 9319 |
| 残基数 n_residues | 1154 |
| 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 | 106.7 Å |
| Rg (实空间) rg_real | 34.02 Å |
| Rg 误差 (实空间) rg_real_error | 0.51 Å |
| I(0) (实空间) i0_real | 2.5770e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.4740e+06 |
| Rg (倒空间) rg_reciprocal | 34.09 Å |
| I(0) (倒空间) i0_reciprocal | 257700000.0000 |
| 解质量估计 total_estimate | 0.6817 |
| 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 | 41.7 Å |
| 偏度 Skewness skewness | 0.197 |
| 峰度 Kurtosis kurtosis | -0.537 |
| 角度范围 angular_range | — – 0.2300 Å−1 |
| 当前正则化参数 α current_alpha | 0.0001 |
| 最高正则化参数 α highest_alpha | 33040000.0000 |
| 实空间数据点数 n_real_points | 47 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 0.038; Positv: 1.000; Valcen: 0.996; Smooth: 0.895 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (5)
6. 折叠分类 (SCOP + CATH) 14 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1it7a1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.20 — tRNA-guanine transglycosylase |
| 家族 Family family | c.1.20.1 — tRNA-guanine transglycosylase |
| 结构域编号 domain_id | d1it7a3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.122 — PUA domain-like |
| 超家族 Superfamily superfamily | b.122.1 — PUA domain-like |
| 家族 Family family | b.122.1.1 — PUA domain |
| 结构域编号 domain_id | d1it7a4 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.17 — Cystatin-like |
| 超家族 Superfamily superfamily | d.17.6 — Pre-PUA domain |
| 家族 Family family | d.17.6.1 — Archaeosine tRNA-guanine transglycosylase, C2 domain |
| 结构域编号 domain_id | d1it7b1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.20 — tRNA-guanine transglycosylase |
| 家族 Family family | c.1.20.1 — tRNA-guanine transglycosylase |
| 结构域编号 domain_id | d1it7b3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.122 — PUA domain-like |
| 超家族 Superfamily superfamily | b.122.1 — PUA domain-like |
| 家族 Family family | b.122.1.1 — PUA domain |
| 结构域编号 domain_id | d1it7b4 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.17 — Cystatin-like |
| 超家族 Superfamily superfamily | d.17.6 — Pre-PUA domain |
| 家族 Family family | d.17.6.1 — Archaeosine tRNA-guanine transglycosylase, C2 domain |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 1it7A01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 105 — Queuine tRNA-ribosyltransferase-like |
| 结构域编号 domain_id | 1it7A02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1020 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — ArcTGT, C1 domain |
| 结构域编号 domain_id | 1it7A03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 450 — Nuclear Transport Factor 2; Chain: A, |
| 同源超家族 H-superfamily homologous superfamily | 90 — ArcTGT, C2 domain |
| 结构域编号 domain_id | 1it7A04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 130 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 |
| 同源超家族 H-superfamily homologous superfamily | 10 — PUA domain |
| 结构域编号 domain_id | 1it7B01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 105 — Queuine tRNA-ribosyltransferase-like |
| 结构域编号 domain_id | 1it7B02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1020 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — ArcTGT, C1 domain |
| 结构域编号 domain_id | 1it7B03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 450 — Nuclear Transport Factor 2; Chain: A, |
| 同源超家族 H-superfamily homologous superfamily | 90 — ArcTGT, C2 domain |
| 结构域编号 domain_id | 1it7B04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 130 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 |
| 同源超家族 H-superfamily homologous superfamily | 10 — PUA domain |