1wu7
Crystal structure of histidyl-tRNA synthetase from Thermoplasma acidophilum
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 | 1wu7 |
| 沉积日期 deposition_date | 2004-12-01 |
| 结构标题 title | Crystal structure of histidyl-tRNA synthetase from Thermoplasma acidophilum |
| 关键词 keywords | LIGASE, structural genomics, dimer; 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 | 31.42 Å |
| 回转半径 Rg (电子) rg_electron | 30.45 Å |
| 零角强度 I(0) i0 | 154943000.00 |
| 分子量 molecular_weight | 96620.0 kDa |
| 排除体积 excluded_volume | 119440 ų |
| 包络体积 envelope_volume | 146930 ų |
| 水化壳体积 shell_volume | 40513 ų |
| 包络直径 envelope_diameter | 109.1 Å |
| 壳层 Rg shell_rg | 37.24 Å |
| 包络 Rg envelope_rg | 30.53 Å |
| 形状 Rg shape_rg | 30.37 Å |
| 总 Rg total_rg | 31.23 Å |
| 总原子数 total_atoms | 6711 |
| 残基数 n_residues | 818 |
| 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 | 102.9 Å |
| Rg (实空间) rg_real | 31.43 Å |
| Rg 误差 (实空间) rg_real_error | 0.81 Å |
| I(0) (实空间) i0_real | 1.5490e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.4730e+06 |
| Rg (倒空间) rg_reciprocal | 31.43 Å |
| I(0) (倒空间) i0_reciprocal | 154900000.0000 |
| 解质量估计 total_estimate | 0.8821 |
| 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 | 37.0 Å |
| 偏度 Skewness skewness | 0.381 |
| 峰度 Kurtosis kurtosis | -0.261 |
| 角度范围 angular_range | — – 0.2500 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 36100000.0000 |
| 实空间数据点数 n_real_points | 51 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.812 |
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) 10 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1wu7a1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.51 — Anticodon-binding domain-like |
| 超家族 Superfamily superfamily | c.51.1 — Class II aaRS ABD-related |
| 家族 Family family | c.51.1.1 — Anticodon-binding domain of Class II aaRS |
| 结构域编号 domain_id | d1wu7a2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.104 — Class II aaRS and biotin synthetases |
| 超家族 Superfamily superfamily | d.104.1 — Class II aaRS and biotin synthetases |
| 家族 Family family | d.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain |
| 结构域编号 domain_id | d1wu7b1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.51 — Anticodon-binding domain-like |
| 超家族 Superfamily superfamily | c.51.1 — Class II aaRS ABD-related |
| 家族 Family family | c.51.1.1 — Anticodon-binding domain of Class II aaRS |
| 结构域编号 domain_id | d1wu7b2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.104 — Class II aaRS and biotin synthetases |
| 超家族 Superfamily superfamily | d.104.1 — Class II aaRS and biotin synthetases |
| 家族 Family family | d.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1wu7A01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 930 — BirA Bifunctional Protein; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Bira Bifunctional Protein; Domain 2 |
| 结构域编号 domain_id | 1wu7A02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 240 — CRO Repressor |
| 同源超家族 H-superfamily homologous superfamily | 30 — |
| 结构域编号 domain_id | 1wu7A03 |
| 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 | 800 — Anticodon-binding domain |
| 结构域编号 domain_id | 1wu7B01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 930 — BirA Bifunctional Protein; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Bira Bifunctional Protein; Domain 2 |
| 结构域编号 domain_id | 1wu7B02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 240 — CRO Repressor |
| 同源超家族 H-superfamily homologous superfamily | 30 — |
| 结构域编号 domain_id | 1wu7B03 |
| 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 | 800 — Anticodon-binding domain |