1x6m
Crystal structure of the glutathione-dependent formaldehyde-activating enzyme (Gfa)
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 | 1x6m |
| 沉积日期 deposition_date | 2004-08-11 |
| 结构标题 title | Crystal structure of the glutathione-dependent formaldehyde-activating enzyme (Gfa) |
| 关键词 keywords | zn-enzyme, formaldehyde, 3_10 helix, LYASE; LYASE |
| 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 | 33.07 Å |
| 回转半径 Rg (电子) rg_electron | 32.12 Å |
| 零角强度 I(0) i0 | 131534000.00 |
| 分子量 molecular_weight | 85824.0 kDa |
| 排除体积 excluded_volume | 105130 ų |
| 包络体积 envelope_volume | 142080 ų |
| 水化壳体积 shell_volume | 37844 ų |
| 包络直径 envelope_diameter | 103.2 Å |
| 壳层 Rg shell_rg | 38.22 Å |
| 包络 Rg envelope_rg | 31.40 Å |
| 形状 Rg shape_rg | 32.09 Å |
| 总 Rg total_rg | 32.70 Å |
| 总原子数 total_atoms | 5977 |
| 残基数 n_residues | 780 |
| 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 | 103.3 Å |
| Rg (实空间) rg_real | 32.97 Å |
| Rg 误差 (实空间) rg_real_error | 0.77 Å |
| I(0) (实空间) i0_real | 1.3150e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.0030e+06 |
| Rg (倒空间) rg_reciprocal | 33.02 Å |
| I(0) (倒空间) i0_reciprocal | 131500000.0000 |
| 解质量估计 total_estimate | 0.9111 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 38.8 Å |
| 偏度 Skewness skewness | 0.181 |
| 峰度 Kurtosis kurtosis | -0.608 |
| 角度范围 angular_range | — – 0.2400 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 10920000.0000 |
| 实空间数据点数 n_real_points | 49 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.931 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (5)
6. 折叠分类 (SCOP + CATH) 12 domains
SCOP 2.08 (8 domains)
| 结构域编号 domain_id | d1x6ma1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.88 — Mss4-like |
| 超家族 Superfamily superfamily | b.88.1 — Mss4-like |
| 家族 Family family | b.88.1.4 — Glutathione-dependent formaldehyde-activating enzyme, Gfa |
| 结构域编号 domain_id | d1x6ma2 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d1x6mb1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.88 — Mss4-like |
| 超家族 Superfamily superfamily | b.88.1 — Mss4-like |
| 家族 Family family | b.88.1.4 — Glutathione-dependent formaldehyde-activating enzyme, Gfa |
| 结构域编号 domain_id | d1x6mb2 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d1x6mc1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.88 — Mss4-like |
| 超家族 Superfamily superfamily | b.88.1 — Mss4-like |
| 家族 Family family | b.88.1.4 — Glutathione-dependent formaldehyde-activating enzyme, Gfa |
| 结构域编号 domain_id | d1x6mc2 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d1x6md1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.88 — Mss4-like |
| 超家族 Superfamily superfamily | b.88.1 — Mss4-like |
| 家族 Family family | b.88.1.4 — Glutathione-dependent formaldehyde-activating enzyme, Gfa |
| 结构域编号 domain_id | d1x6md2 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 1x6mA00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1590 — glutathione-dependent formaldehyde- activating enzyme (gfa) |
| 同源超家族 H-superfamily homologous superfamily | 10 — glutathione-dependent formaldehyde- activating enzyme (gfa) |
| 结构域编号 domain_id | 1x6mB00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1590 — glutathione-dependent formaldehyde- activating enzyme (gfa) |
| 同源超家族 H-superfamily homologous superfamily | 10 — glutathione-dependent formaldehyde- activating enzyme (gfa) |
| 结构域编号 domain_id | 1x6mC00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1590 — glutathione-dependent formaldehyde- activating enzyme (gfa) |
| 同源超家族 H-superfamily homologous superfamily | 10 — glutathione-dependent formaldehyde- activating enzyme (gfa) |
| 结构域编号 domain_id | 1x6mD00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1590 — glutathione-dependent formaldehyde- activating enzyme (gfa) |
| 同源超家族 H-superfamily homologous superfamily | 10 — glutathione-dependent formaldehyde- activating enzyme (gfa) |