1pj6
Crystal structure of dimethylglycine oxidase of Arthrobacter globiformis in complex with folic acid
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 | 1pj6 |
| 沉积日期 deposition_date | 2003-06-01 |
| 结构标题 title | Crystal structure of dimethylglycine oxidase of Arthrobacter globiformis in complex with folic acid |
| 关键词 keywords | channelling, folate binding, FAD binding, amine oxidation, OXIDOREDUCTASE; OXIDOREDUCTASE |
| 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 | 28.86 Å |
| 回转半径 Rg (电子) rg_electron | 27.90 Å |
| 零角强度 I(0) i0 | 132519000.00 |
| 分子量 molecular_weight | 90336.0 kDa |
| 排除体积 excluded_volume | 112700 ų |
| 包络体积 envelope_volume | 133390 ų |
| 水化壳体积 shell_volume | 39182 ų |
| 包络直径 envelope_diameter | 96.5 Å |
| 壳层 Rg shell_rg | 36.08 Å |
| 包络 Rg envelope_rg | 27.69 Å |
| 形状 Rg shape_rg | 27.89 Å |
| 总 Rg total_rg | 28.68 Å |
| 总原子数 total_atoms | 6371 |
| 残基数 n_residues | 828 |
| 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 | 90.9 Å |
| Rg (实空间) rg_real | 28.76 Å |
| Rg 误差 (实空间) rg_real_error | 0.59 Å |
| I(0) (实空间) i0_real | 1.3250e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.8080e+06 |
| Rg (倒空间) rg_reciprocal | 28.81 Å |
| I(0) (倒空间) i0_reciprocal | 132500000.0000 |
| 解质量估计 total_estimate | 0.9030 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 34.7 Å |
| 偏度 Skewness skewness | 0.242 |
| 峰度 Kurtosis kurtosis | -0.446 |
| 角度范围 angular_range | — – 0.2750 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 33480000.0000 |
| 实空间数据点数 n_real_points | 56 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.971 |
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) 9 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1pj6a1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.44 — Elongation factor/aminomethyltransferase common domain |
| 超家族 Superfamily superfamily | b.44.2 — Aminomethyltransferase beta-barrel domain |
| 家族 Family family | b.44.2.1 — Aminomethyltransferase beta-barrel domain |
| 结构域编号 domain_id | d1pj6a2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.3 — FAD/NAD(P)-binding domain |
| 超家族 Superfamily superfamily | c.3.1 — FAD/NAD(P)-binding domain |
| 家族 Family family | c.3.1.2 — FAD-linked reductases, N-terminal domain |
| 结构域编号 domain_id | d1pj6a3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.16 — FAD-linked reductases, C-terminal domain |
| 超家族 Superfamily superfamily | d.16.1 — FAD-linked reductases, C-terminal domain |
| 家族 Family family | d.16.1.5 — L-aminoacid/polyamine oxidase |
| 结构域编号 domain_id | d1pj6a4 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.250 — Folate-binding domain |
| 超家族 Superfamily superfamily | d.250.1 — Folate-binding domain |
| 家族 Family family | d.250.1.1 — Aminomethyltransferase folate-binding domain |
CATH v4.4 (5 domains)
| 结构域编号 domain_id | 1pj6A01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 50 — FAD/NAD(P)-binding domain |
| 同源超家族 H-superfamily homologous superfamily | 60 — FAD/NAD(P)-binding domain |
| 结构域编号 domain_id | 1pj6A02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 9 — D-Amino Acid Oxidase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — D-Amino Acid Oxidase, subunit A, domain 2 |
| 结构域编号 domain_id | 1pj6A03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1360 — Gyrase A; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 120 — Probable tRNA modification gtpase trme; domain 1 |
| 结构域编号 domain_id | 1pj6A04 |
| 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 | 1400 — Aminomethyltransferase beta-barrel domains |
| 结构域编号 domain_id | 1pj6A05 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 30 — Elongation Factor Tu (Ef-tu); domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 110 — Aminomethyltransferase beta-barrel domains |