1irx
Crystal structure of class I lysyl-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 | 1irx |
| 沉积日期 deposition_date | 2001-10-25 |
| 结构标题 title | Crystal structure of class I lysyl-tRNA synthetase |
| 关键词 keywords | ;beta sandwitch, zinc-binding structure, Rossmann fold, alpha-helix cage, 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 | 44.55 Å |
| 回转半径 Rg (电子) rg_electron | 44.99 Å |
| 零角强度 I(0) i0 | 208882000.00 |
| 分子量 molecular_weight | 120340.0 kDa |
| 排除体积 excluded_volume | 151580 ų |
| 包络体积 envelope_volume | 209840 ų |
| 水化壳体积 shell_volume | 43723 ų |
| 包络直径 envelope_diameter | 164.3 Å |
| 壳层 Rg shell_rg | 42.94 Å |
| 包络 Rg envelope_rg | 44.45 Å |
| 形状 Rg shape_rg | 44.97 Å |
| 总 Rg total_rg | 44.95 Å |
| 总原子数 total_atoms | 8506 |
| 残基数 n_residues | 1015 |
| 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 | 155.4 Å |
| Rg (实空间) rg_real | 45.23 Å |
| Rg 误差 (实空间) rg_real_error | 1.81 Å |
| I(0) (实空间) i0_real | 2.0890e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.7460e+06 |
| Rg (倒空间) rg_reciprocal | 44.56 Å |
| I(0) (倒空间) i0_reciprocal | 208700000.0000 |
| 解质量估计 total_estimate | 0.5357 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 35.5 Å |
| 偏度 Skewness skewness | 0.645 |
| 峰度 Kurtosis kurtosis | -0.059 |
| 角度范围 angular_range | — – 0.1750 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 16980000.0000 |
| 实空间数据点数 n_real_points | 36 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.697; Stabil: 0.998; Sysdev: 0.062; Positv: 1.000; Valcen: 0.524; Smooth: 0.165 |
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) 14 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1irxa1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.97 — An anticodon-binding domain of class I aminoacyl-tRNA synthetases |
| 超家族 Superfamily superfamily | a.97.1 — An anticodon-binding domain of class I aminoacyl-tRNA synthetases |
| 家族 Family family | a.97.1.2 — C-terminal domain of class I lysyl-tRNA synthetase |
| 结构域编号 domain_id | d1irxa2 |
| 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 | d1irxb1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.97 — An anticodon-binding domain of class I aminoacyl-tRNA synthetases |
| 超家族 Superfamily superfamily | a.97.1 — An anticodon-binding domain of class I aminoacyl-tRNA synthetases |
| 家族 Family family | a.97.1.2 — C-terminal domain of class I lysyl-tRNA synthetase |
| 结构域编号 domain_id | d1irxb2 |
| 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 (10 domains)
| 结构域编号 domain_id | 1irxA01 |
| 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 |
| 结构域编号 domain_id | 1irxA02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 30 — SH3 type barrels. |
| 同源超家族 H-superfamily homologous superfamily | 300 — class i lysyl-tRNA synthetase like |
| 结构域编号 domain_id | 1irxA03 |
| 类 Class class | 6 — Special |
| 架构 Architecture architecture | 10 — Helix non-globular |
| 拓扑 Topology topology | 20 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Lysine tRNA ligase, stem contact fold domain |
| 结构域编号 domain_id | 1irxA04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 770 — |
| 结构域编号 domain_id | 1irxA05 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 350 — |
| 结构域编号 domain_id | 1irxB01 |
| 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 |
| 结构域编号 domain_id | 1irxB02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 30 — SH3 type barrels. |
| 同源超家族 H-superfamily homologous superfamily | 300 — class i lysyl-tRNA synthetase like |
| 结构域编号 domain_id | 1irxB03 |
| 类 Class class | 6 — Special |
| 架构 Architecture architecture | 10 — Helix non-globular |
| 拓扑 Topology topology | 20 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Lysine tRNA ligase, stem contact fold domain |
| 结构域编号 domain_id | 1irxB04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 770 — |
| 结构域编号 domain_id | 1irxB05 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 350 — |