1iyw
Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-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 | 1iyw |
| 沉积日期 deposition_date | 2002-09-10 |
| 结构标题 title | Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase |
| 关键词 keywords | Rossmann Fold, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, 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 | 92.66 Å |
| 回转半径 Rg (电子) rg_electron | 93.24 Å |
| 零角强度 I(0) i0 | 523049000.00 |
| 分子量 molecular_weight | 197550.0 kDa |
| 排除体积 excluded_volume | 242600 ų |
| 包络体积 envelope_volume | 430370 ų |
| 水化壳体积 shell_volume | 39887 ų |
| 包络直径 envelope_diameter | 244.0 Å |
| 壳层 Rg shell_rg | 100.20 Å |
| 包络 Rg envelope_rg | 79.22 Å |
| 形状 Rg shape_rg | 93.27 Å |
| 总 Rg total_rg | 93.29 Å |
| 总原子数 total_atoms | — |
| 残基数 n_residues | — |
| 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 | 310.1 Å |
| Rg (实空间) rg_real | 93.41 Å |
| Rg 误差 (实空间) rg_real_error | 4.42 Å |
| I(0) (实空间) i0_real | 5.2300e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.2180e+07 |
| Rg (倒空间) rg_reciprocal | 86.80 Å |
| I(0) (倒空间) i0_reciprocal | 513200000.0000 |
| 解质量估计 total_estimate | 0.5758 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 4 |
| 主峰位置 r_peak_primary | 182.4 Å |
| 偏度 Skewness skewness | -0.031 |
| 峰度 Kurtosis kurtosis | -1.671 |
| 角度范围 angular_range | — – 0.0850 Å−1 |
| 当前正则化参数 α current_alpha | 0.0001 |
| 最高正则化参数 α highest_alpha | 12350000.0000 |
| 实空间数据点数 n_real_points | 18 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.000; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.484; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (1)
6. 折叠分类 (SCOP + CATH) 8 domains
SCOP 2.08 (8 domains)
| 结构域编号 domain_id | d1iywa1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.2 — Long alpha-hairpin |
| 超家族 Superfamily superfamily | a.2.7 — tRNA-binding arm |
| 家族 Family family | a.2.7.3 — Valyl-tRNA synthetase (ValRS) C-terminal domain |
| 结构域编号 domain_id | d1iywa2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.27 — Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases |
| 超家族 Superfamily superfamily | a.27.1 — Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases |
| 家族 Family family | a.27.1.1 — Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases |
| 结构域编号 domain_id | d1iywa3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.51 — ValRS/IleRS/LeuRS editing domain |
| 超家族 Superfamily superfamily | b.51.1 — ValRS/IleRS/LeuRS editing domain |
| 家族 Family family | b.51.1.1 — ValRS/IleRS/LeuRS editing domain |
| 结构域编号 domain_id | d1iywa4 |
| 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 |
| 结构域编号 domain_id | d1iywb1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.2 — Long alpha-hairpin |
| 超家族 Superfamily superfamily | a.2.7 — tRNA-binding arm |
| 家族 Family family | a.2.7.3 — Valyl-tRNA synthetase (ValRS) C-terminal domain |
| 结构域编号 domain_id | d1iywb2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.27 — Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases |
| 超家族 Superfamily superfamily | a.27.1 — Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases |
| 家族 Family family | a.27.1.1 — Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases |
| 结构域编号 domain_id | d1iywb3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.51 — ValRS/IleRS/LeuRS editing domain |
| 超家族 Superfamily superfamily | b.51.1 — ValRS/IleRS/LeuRS editing domain |
| 家族 Family family | b.51.1.1 — ValRS/IleRS/LeuRS editing domain |
| 结构域编号 domain_id | d1iywb4 |
| 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 |