1nyl
Unliganded glutaminyl-tRNA synthetase
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 | 1nyl |
| 沉积日期 deposition_date | 2003-02-12 |
| 结构标题 title | Unliganded glutaminyl-tRNA synthetase |
| 关键词 keywords | LIGASE; LIGASE |
| 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 | 30.94 Å |
| 回转半径 Rg (电子) rg_electron | 31.11 Å |
| 零角强度 I(0) i0 | 58432200.00 |
| 分子量 molecular_weight | 59112.0 kDa |
| 排除体积 excluded_volume | 73498 ų |
| 包络体积 envelope_volume | 96185 ų |
| 水化壳体积 shell_volume | 28553 ų |
| 包络直径 envelope_diameter | 111.0 Å |
| 壳层 Rg shell_rg | 34.60 Å |
| 包络 Rg envelope_rg | 31.01 Å |
| 形状 Rg shape_rg | 31.10 Å |
| 总 Rg total_rg | 31.47 Å |
| 总原子数 total_atoms | 4168 |
| 残基数 n_residues | 523 |
| 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 | 106.1 Å |
| Rg (实空间) rg_real | 31.33 Å |
| Rg 误差 (实空间) rg_real_error | 1.09 Å |
| I(0) (实空间) i0_real | 5.8430e+07 |
| I(0) 误差 (实空间) i0_real_error | 8.9230e+05 |
| Rg (倒空间) rg_reciprocal | 31.17 Å |
| I(0) (倒空间) i0_reciprocal | 58420000.0000 |
| 解质量估计 total_estimate | 0.8068 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 29.1 Å |
| 偏度 Skewness skewness | 0.608 |
| 峰度 Kurtosis kurtosis | -0.250 |
| 角度范围 angular_range | — – 0.2550 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 9579000.0000 |
| 实空间数据点数 n_real_points | 52 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.717; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.614; Smooth: 0.718 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (2)
6. 折叠分类 (SCOP + CATH) 7 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d1nyla1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.53 — Ribosomal protein L25-like |
| 超家族 Superfamily superfamily | b.53.1 — Ribosomal protein L25-like |
| 家族 Family family | b.53.1.2 — Gln-tRNA synthetase (GlnRS), C-terminal (anticodon-binding) domain |
| 结构域编号 domain_id | d1nyla2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.26 — Adenine nucleotide alpha hydrolase-like |
| 超家族 Superfamily superfamily | c.26.1 — Nucleotidylyl transferase |
| 家族 Family family | c.26.1.1 — Class I aminoacyl-tRNA synthetases (RS), catalytic domain |
CATH v4.4 (5 domains)
| 结构域编号 domain_id | 1nylA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 240 — Ribosomal Protein L25; Chain P |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ribosomal Protein L25; Chain P |
| 结构域编号 domain_id | 1nylA02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 240 — Ribosomal Protein L25; Chain P |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ribosomal Protein L25; Chain P |
| 结构域编号 domain_id | 1nylA03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1160 — Glutamyl-tRNA Synthetase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Glutamyl-trna Synthetase; Domain 2 |
| 结构域编号 domain_id | 1nylA04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 800 — Glutamyl-tRNA Synthetase; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Glutamyl-tRNA Synthetase; Domain 3 |
| 结构域编号 domain_id | 1nylA05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 620 — HUPs |