1oy5
Crystal structure of tRNA (m1G37) methyltransferase from Aquifex aeolicus
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 | 1oy5 |
| 沉积日期 deposition_date | 2003-04-03 |
| 结构标题 title | Crystal structure of tRNA (m1G37) methyltransferase from Aquifex aeolicus |
| 关键词 keywords | ;structural genomics, trmD, tRNA (m1G37) methyltransferase, BSGC structure funded by NIH, Protein Structure Initiative, PSI, Berkeley Structural Genomics Center, TRANSFERASE ;; TRANSFERASE |
| 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 | 36.02 Å |
| 回转半径 Rg (电子) rg_electron | 35.85 Å |
| 零角强度 I(0) i0 | 77170300.00 |
| 分子量 molecular_weight | 75087.0 kDa |
| 排除体积 excluded_volume | 96340 ų |
| 包络体积 envelope_volume | 140860 ų |
| 水化壳体积 shell_volume | 34153 ų |
| 包络直径 envelope_diameter | 124.0 Å |
| 壳层 Rg shell_rg | 39.65 Å |
| 包络 Rg envelope_rg | 37.41 Å |
| 形状 Rg shape_rg | 35.85 Å |
| 总 Rg total_rg | 36.17 Å |
| 总原子数 total_atoms | 5303 |
| 残基数 n_residues | 654 |
| 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 | 125.2 Å |
| Rg (实空间) rg_real | 36.38 Å |
| Rg 误差 (实空间) rg_real_error | 1.26 Å |
| I(0) (实空间) i0_real | 7.7170e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.4660e+06 |
| Rg (倒空间) rg_reciprocal | 36.16 Å |
| I(0) (倒空间) i0_reciprocal | 77150000.0000 |
| 解质量估计 total_estimate | 0.8215 |
| 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 | 34.1 Å |
| 偏度 Skewness skewness | 0.538 |
| 峰度 Kurtosis kurtosis | -0.366 |
| 角度范围 angular_range | — – 0.2200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 9978000.0000 |
| 实空间数据点数 n_real_points | 45 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.737; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.677; Smooth: 0.789 |
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) 9 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d1oy5a_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.116 — alpha/beta knot |
| 超家族 Superfamily superfamily | c.116.1 — alpha/beta knot |
| 家族 Family family | c.116.1.4 — tRNA(m1G37)-methyltransferase TrmD |
| 结构域编号 domain_id | d1oy5b_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.116 — alpha/beta knot |
| 超家族 Superfamily superfamily | c.116.1 — alpha/beta knot |
| 家族 Family family | c.116.1.4 — tRNA(m1G37)-methyltransferase TrmD |
| 结构域编号 domain_id | d1oy5c_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.116 — alpha/beta knot |
| 超家族 Superfamily superfamily | c.116.1 — alpha/beta knot |
| 家族 Family family | c.116.1.4 — tRNA(m1G37)-methyltransferase TrmD |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1oy5A01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1280 — Alpha/beta knot |
| 同源超家族 H-superfamily homologous superfamily | 10 — SPOUT methyltransferase, trefoil knot domain |
| 结构域编号 domain_id | 1oy5A02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1270 — Trp Operon Repressor; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — tRNA(m1g37)methyltransferase, domain 2 |
| 结构域编号 domain_id | 1oy5B01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1280 — Alpha/beta knot |
| 同源超家族 H-superfamily homologous superfamily | 10 — SPOUT methyltransferase, trefoil knot domain |
| 结构域编号 domain_id | 1oy5B02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1270 — Trp Operon Repressor; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — tRNA(m1g37)methyltransferase, domain 2 |
| 结构域编号 domain_id | 1oy5C01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1280 — Alpha/beta knot |
| 同源超家族 H-superfamily homologous superfamily | 10 — SPOUT methyltransferase, trefoil knot domain |
| 结构域编号 domain_id | 1oy5C02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1270 — Trp Operon Repressor; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — tRNA(m1g37)methyltransferase, domain 2 |