2akw
Crystal Structure of T.Thermophilus Phenylalanyl-tRNA synthetase complexed with p-Cl-Phenylalanine
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 | 2akw |
| 沉积日期 deposition_date | 2005-08-04 |
| 结构标题 title | Crystal Structure of T.Thermophilus Phenylalanyl-tRNA synthetase complexed with p-Cl-Phenylalanine |
| 关键词 keywords | protein-unnatural amino acid complex, 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 | 38.34 Å |
| 回转半径 Rg (电子) rg_electron | 38.48 Å |
| 零角强度 I(0) i0 | 197013000.00 |
| 分子量 molecular_weight | 116850.0 kDa |
| 排除体积 excluded_volume | 147670 ų |
| 包络体积 envelope_volume | 196280 ų |
| 水化壳体积 shell_volume | 44862 ų |
| 包络直径 envelope_diameter | 141.6 Å |
| 壳层 Rg shell_rg | 41.48 Å |
| 包络 Rg envelope_rg | 39.08 Å |
| 形状 Rg shape_rg | 38.47 Å |
| 总 Rg total_rg | 38.71 Å |
| 总原子数 total_atoms | 8269 |
| 残基数 n_residues | 1051 |
| 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 | 136.8 Å |
| Rg (实空间) rg_real | 38.79 Å |
| Rg 误差 (实空间) rg_real_error | 1.33 Å |
| I(0) (实空间) i0_real | 1.9700e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.8150e+06 |
| Rg (倒空间) rg_reciprocal | 38.51 Å |
| I(0) (倒空间) i0_reciprocal | 197000000.0000 |
| 解质量估计 total_estimate | 0.8085 |
| 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 | 36.7 Å |
| 偏度 Skewness skewness | 0.625 |
| 峰度 Kurtosis kurtosis | 0.001 |
| 角度范围 angular_range | — – 0.2050 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 37470000.0000 |
| 实空间数据点数 n_real_points | 42 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.712; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.828; Smooth: 0.541 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (6)
6. 折叠分类 (SCOP + CATH) 14 domains
SCOP 2.08 (7 domains)
| 结构域编号 domain_id | d2akwa_ |
| 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 | d2akwb1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.6 — Putative DNA-binding domain |
| 超家族 Superfamily superfamily | a.6.1 — Putative DNA-binding domain |
| 家族 Family family | a.6.1.1 — Domains B1 and B5 of PheRS-beta, PheT |
| 结构域编号 domain_id | d2akwb2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.6 — Putative DNA-binding domain |
| 超家族 Superfamily superfamily | a.6.1 — Putative DNA-binding domain |
| 家族 Family family | a.6.1.1 — Domains B1 and B5 of PheRS-beta, PheT |
| 结构域编号 domain_id | d2akwb3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.40 — OB-fold |
| 超家族 Superfamily superfamily | b.40.4 — Nucleic acid-binding proteins |
| 家族 Family family | b.40.4.4 — Myf domain |
| 结构域编号 domain_id | d2akwb4 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.153 — PheT/TilS domain |
| 超家族 Superfamily superfamily | b.153.1 — PheT/TilS domain |
| 家族 Family family | b.153.1.1 — B3/B4 domain of PheRS, PheT |
| 结构域编号 domain_id | d2akwb5 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.13 — Anticodon-binding domain of PheRS |
| 家族 Family family | d.58.13.1 — Anticodon-binding domain of PheRS |
| 结构域编号 domain_id | d2akwb6 |
| 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 (7 domains)
| 结构域编号 domain_id | 2akwA00 |
| 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 | 2akwB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — |
| 结构域编号 domain_id | 2akwB02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P) |
| 同源超家族 H-superfamily homologous superfamily | 140 — Nucleic acid-binding proteins |
| 结构域编号 domain_id | 2akwB03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 40 — Phenylalanyl-tRNA Synthetase; Chain B, domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Phenylalanyl-trna Synthetase, Chain B, domain 3 |
| 结构域编号 domain_id | 2akwB04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — |
| 结构域编号 domain_id | 2akwB05 |
| 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 | 2akwB06 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 380 — Ferrodoxin-fold anticodon-binding domain |